5OPX
Crystal structure of the GroEL mutant A109C in complex with GroES and ADP BeF2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4PKN | pdbid 4PKN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 291 | 10 mM ATP, 3 mM BeF2, 0.1 M Tris, pH 8.0, 0.2 M NaCl and 20 % PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.11 | 60.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 217.567 | α = 90 |
b = 230.504 | β = 90 |
c = 235.391 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 2M | 2016-08-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.96600 | ESRF | MASSIF-1 |
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 | |||||
1 | 3.64 | 50.01 | 99.8 | 0.165 | 0.185 | 0.08 | 0.997 | 7.9 | 4.9 | 132375 |
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) | ||||||||
1 | 3.64 | 3.7 | 99.9 | 1.161 | 1.294 | 0.557 | 0.545 | 5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdbid 4PKN | 3.64 | 50.01 | 125728 | 6583 | 99.69 | 0.2324 | 0.2312 | 0.23 | 0.256 | 0.25 | RANDOM | 137.055 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.94 | 3.43 | -4.37 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.151 |
r_dihedral_angle_4_deg | 19.619 |
r_dihedral_angle_3_deg | 16.107 |
r_dihedral_angle_1_deg | 5.636 |
r_angle_refined_deg | 1.588 |
r_angle_other_deg | 1 |
r_chiral_restr | 0.08 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 63403 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 462 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |