BMP-9 Wild-Type Dimer without Radiation Damage in Acidic pH
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 1ZKZ | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, HANGING DROP | 3.5 | 289.15 | 1M NaCl, 3.5% PEG8K, 0.3M Sodium Citrate pH 3.5 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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3.79 | 67.54 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 71.045 | α = 90 |
b = 71.045 | β = 90 |
c = 145.567 | γ = 90 |
Symmetry |
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Space Group | I 41 2 2 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | | 2022-04-24 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1 | APS | 22-ID |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | fixed target |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 |
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1 | 2.35 | 41.34 | 97.9 | 0.209 | 0.251 | 0.135 | 0.982 | 4.8 | 5 | | 7868 | | | 40.38 |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 2.35 | 2.43 | 98.3 | | 1.478 | 1.785 | 0.973 | 0.311 | 1.7 | 4.6 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.35 | 41.34 | 1.01 | 7852 | 438 | 96.56 | 0.2027 | 0.2 | 0.2013 | 0.2489 | 0.2498 | 60.41 |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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| | | | | |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 10.1613 |
f_angle_d | 0.8225 |
f_chiral_restr | 0.0411 |
f_bond_d | 0.0054 |
f_plane_restr | 0.0045 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 826 |
Nucleic Acid Atoms | |
Solvent Atoms | 62 |
Heterogen Atoms | 28 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |