SFX 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 |
|---|
| 2.95 | 63.6 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 107.1 | α = 90 |
| b = 107.1 | β = 90 |
| c = 107.1 | 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 | 300 | CCD | MPCCD | | 2019-06-26 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.127 | SACLA | BL2 |
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 chips | | | Geobrick and Smaract | | |
| Measurement |
|---|
| Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
|---|
| 1 | 10 (fs) | 30 | 2.56 | 11 (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 | 1.8 | 33.89 | 100 | 0.938 | 0.204 | 4 | 233.7 | | 38160 | | | |
| 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 | 1.9 | 1.93 | 100 | | 0.639 | 0.492 | 2.1 | 159.9 | |
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 | 1.8 | 33.89 | 38147 | 1886 | 99.945 | 0.191 | 0.19 | 0.19 | 0.219 | 0.2191 | 29.718 |
| 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 | 16.031 |
| r_dihedral_angle_3_deg | 12.124 |
| r_lrange_it | 7.434 |
| r_lrange_other | 7.401 |
| r_dihedral_angle_1_deg | 6.846 |
| r_dihedral_angle_2_deg | 6.572 |
| r_scangle_it | 4.825 |
| r_scangle_other | 4.823 |
| r_scbond_other | 3.124 |
| r_scbond_it | 3.123 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_6_deg | 16.031 |
| r_dihedral_angle_3_deg | 12.124 |
| r_lrange_it | 7.434 |
| r_lrange_other | 7.401 |
| r_dihedral_angle_1_deg | 6.846 |
| r_dihedral_angle_2_deg | 6.572 |
| r_scangle_it | 4.825 |
| r_scangle_other | 4.823 |
| r_scbond_other | 3.124 |
| r_scbond_it | 3.123 |
| r_angle_refined_deg | 2.317 |
| r_mcangle_other | 2.309 |
| r_mcangle_it | 2.307 |
| r_mcbond_it | 1.611 |
| r_mcbond_other | 1.611 |
| r_angle_other_deg | 0.628 |
| r_nbd_refined | 0.204 |
| r_symmetry_nbd_other | 0.201 |
| r_nbd_other | 0.195 |
| r_nbtor_refined | 0.182 |
| r_symmetry_nbd_refined | 0.182 |
| r_symmetry_xyhbond_nbd_refined | 0.124 |
| r_xyhbond_nbd_refined | 0.121 |
| r_symmetry_nbtor_other | 0.088 |
| r_chiral_restr | 0.087 |
| r_bond_refined_d | 0.017 |
| r_gen_planes_other | 0.014 |
| r_gen_planes_refined | 0.013 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2126 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 109 |
| Heterogen Atoms | 105 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| CrystFEL | data reduction |
| PRIME | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| Coot | model building |