McCP in complex with photocaged nitric oxide, 1.44 s, 9.5 microjoule, SSX
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6HIH | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | | 291 | Final concentrations: 20 mg/mL protein, 50 mM HEPES pH 7.5, 34 % (v/v) polyethylene glycol 550, 500 mM MES pH 6.5, 5 mM ZnSO4. |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.95 | 58.36 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 107.183 | α = 90 |
| b = 107.183 | β = 90 |
| c = 107.183 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 3 |
|---|
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 | | 2021-09-30 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 1.00 | 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 | 75.91 | 100 | 0.992 | 0.122 | 5.8 | 63 | | 28000 | | | |
| 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 | 2.03 | 100 | | 0.366 | 1.042 | 0.7 | 48.8 | |
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 | 75.905 | 28000 | 1332 | 100 | 0.163 | 0.1617 | 0.1617 | 0.1942 | 0.1942 | 37.22 |
| 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] |
|---|
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_6_deg | 14.751 |
| r_dihedral_angle_3_deg | 14.138 |
| r_lrange_it | 9.724 |
| r_scangle_it | 8.889 |
| r_dihedral_angle_2_deg | 7.006 |
| r_dihedral_angle_1_deg | 6.906 |
| r_scbond_it | 5.826 |
| r_mcangle_it | 4.487 |
| r_mcbond_it | 3.347 |
| r_angle_refined_deg | 2.494 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_6_deg | 14.751 |
| r_dihedral_angle_3_deg | 14.138 |
| r_lrange_it | 9.724 |
| r_scangle_it | 8.889 |
| r_dihedral_angle_2_deg | 7.006 |
| r_dihedral_angle_1_deg | 6.906 |
| r_scbond_it | 5.826 |
| r_mcangle_it | 4.487 |
| r_mcbond_it | 3.347 |
| r_angle_refined_deg | 2.494 |
| r_nbtor_refined | 0.317 |
| r_nbd_refined | 0.21 |
| r_symmetry_nbd_refined | 0.201 |
| r_xyhbond_nbd_refined | 0.141 |
| r_chiral_restr | 0.122 |
| r_symmetry_xyhbond_nbd_refined | 0.121 |
| r_gen_planes_refined | 0.011 |
| r_bond_refined_d | 0.01 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2144 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 51 |
| Heterogen Atoms | 92 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| DIALS | data reduction |
| xia2 | data reduction |
| xia2 | data scaling |
| REFMAC | phasing |
| Coot | model building |
| REFMAC | refinement |