DtpB in complex with photocaged nitric oxide, 1.24 s, 16.1 microjoule, SSX
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6YRJ | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | | 291 | 6-10 mg/ml of protein in 50 mm sodium acetate, 150 mm NaCl pH 5 mixed with 150 mM MgCl2, 150 mm HEPES, 20 % PEG 4000, pH 7.5. |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.45 | 49.72 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 87.142 | α = 90 |
| b = 123.022 | β = 90 |
| c = 195.394 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | PIXEL | DECTRIS PILATUS3 6M | | 2023-02-23 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 1.000 | Diamond | I24 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | fixed target |
| Fixed Target |
|---|
| Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
|---|
| 1 | Oxford silicon chip | | | Geobrick and Smaract | | |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | undefined (fs) | | | undefined (KeV) | |
| Data Reduction |
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
|---|
| 1 | | | | |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
|---|
| 1 | 2.4 | 79.713 | 100 | 0.958 | 0.234 | 37.7 | 23.3 | | 82830 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.4 | 2.44 | 100 | | 0.311 | 1.157 | 1.4 | 17.4 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.4 | 79.713 | 82830 | 4184 | 99.976 | 0.194 | 0.1926 | 0.1932 | 0.2119 | 0.2121 | 37.763 |
| Temperature Factor Modeling |
|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
|---|
| -1.123 | | | 0.698 | | 0.425 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 13.633 |
| r_dihedral_angle_6_deg | 11.733 |
| r_dihedral_angle_1_deg | 5.647 |
| r_lrange_it | 4.838 |
| r_dihedral_angle_2_deg | 4.313 |
| r_scangle_it | 2.895 |
| r_mcangle_it | 2.477 |
| r_scbond_it | 1.659 |
| r_mcbond_it | 1.373 |
| r_angle_refined_deg | 1.065 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 13.633 |
| r_dihedral_angle_6_deg | 11.733 |
| r_dihedral_angle_1_deg | 5.647 |
| r_lrange_it | 4.838 |
| r_dihedral_angle_2_deg | 4.313 |
| r_scangle_it | 2.895 |
| r_mcangle_it | 2.477 |
| r_scbond_it | 1.659 |
| r_mcbond_it | 1.373 |
| r_angle_refined_deg | 1.065 |
| r_nbtor_refined | 0.294 |
| r_symmetry_nbd_refined | 0.246 |
| r_symmetry_xyhbond_nbd_refined | 0.216 |
| r_nbd_refined | 0.173 |
| r_xyhbond_nbd_refined | 0.107 |
| r_chiral_restr | 0.083 |
| r_ncsr_local_group_5 | 0.08 |
| r_ncsr_local_group_3 | 0.077 |
| r_ncsr_local_group_14 | 0.076 |
| r_ncsr_local_group_9 | 0.075 |
| r_ncsr_local_group_1 | 0.073 |
| r_ncsr_local_group_7 | 0.072 |
| r_ncsr_local_group_12 | 0.072 |
| r_ncsr_local_group_15 | 0.072 |
| r_ncsr_local_group_2 | 0.07 |
| r_ncsr_local_group_10 | 0.069 |
| r_ncsr_local_group_4 | 0.067 |
| r_ncsr_local_group_13 | 0.067 |
| r_ncsr_local_group_6 | 0.066 |
| r_ncsr_local_group_8 | 0.062 |
| r_ncsr_local_group_11 | 0.062 |
| r_bond_refined_d | 0.003 |
| r_gen_planes_refined | 0.003 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 13975 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 538 |
| Heterogen Atoms | 270 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| DIALS | data reduction |
| xia2 | data reduction |
| xia2 | data scaling |
| MOLREP | phasing |
| Coot | model building |