SSX structure of cytochrome c prime beta from Methylococcus capsulatus (Bath)
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 |
|---|
| 2.96 | 63.6 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 107.227 | α = 90 |
| b = 107.227 | β = 90 |
| c = 107.227 | 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 EIGER2 X CdTe 9M | | 2023-05-17 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.620 | 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 | 2.15 | 75.82 | 100 | 0.984 | 0.188 | 12.9 | 69.9 | | 22647 | | | |
| 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 | 2.15 | 2.19 | 100 | | 0.279 | 1.017 | | 58.1 | |
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 | 2.151 | 61.984 | 22641 | 1097 | 99.996 | 0.198 | 0.1962 | 0.1962 | 0.2371 | 0.2369 | 39.596 |
| 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 | 13.856 |
| r_dihedral_angle_3_deg | 13.484 |
| r_lrange_it | 9.014 |
| r_dihedral_angle_1_deg | 7.623 |
| r_scangle_it | 6.133 |
| r_dihedral_angle_2_deg | 5.535 |
| r_mcangle_it | 4.147 |
| r_scbond_it | 3.905 |
| r_mcbond_it | 2.867 |
| r_angle_refined_deg | 1.667 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_6_deg | 13.856 |
| r_dihedral_angle_3_deg | 13.484 |
| r_lrange_it | 9.014 |
| r_dihedral_angle_1_deg | 7.623 |
| r_scangle_it | 6.133 |
| r_dihedral_angle_2_deg | 5.535 |
| r_mcangle_it | 4.147 |
| r_scbond_it | 3.905 |
| r_mcbond_it | 2.867 |
| r_angle_refined_deg | 1.667 |
| r_nbtor_refined | 0.316 |
| r_symmetry_nbd_refined | 0.303 |
| r_nbd_refined | 0.218 |
| r_xyhbond_nbd_refined | 0.13 |
| r_symmetry_xyhbond_nbd_refined | 0.105 |
| r_chiral_restr | 0.086 |
| r_metal_ion_refined | 0.026 |
| r_bond_refined_d | 0.012 |
| r_gen_planes_refined | 0.009 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2133 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 80 |
| Heterogen Atoms | 99 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| DIALS | data reduction |
| xia2 | data reduction |
| xia2 | data scaling |
| MOLREP | phasing |
| Coot | model building |