8FW6
Human Lactate Dehydrogenase A in Complex with Inhibitor CHK-336
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7M2N |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 4.6 | 291 | 0.1 M Sodium Acetate pH 4.6 30% (v/v) PEG 400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.87 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 118.174 | ¦Á = 90 |
b = 118.174 | ¦Â = 90 |
c = 94.788 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 PILATUS 200K | 2019-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (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 | 2.34 | 50 | 100 | 0.175 | 0.181 | 14 | 13.8 | 32736 | 29.35 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.34 | 2.38 | 100 | 0.737 | 0.805 | 0.76 | 2.29 | 6.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.34 | 45.07 | 30951 | 1562 | 99.38 | 0.15601 | 0.15356 | 0.20598 | RANDOM | 33.609 |
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] | |
-0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 15.034 |
r_dihedral_angle_2_deg | 11.642 |
r_long_range_B_other | 7.048 |
r_long_range_B_refined | 7.046 |
r_dihedral_angle_1_deg | 6.927 |
r_scangle_other | 5.389 |
r_mcangle_it | 3.918 |
r_mcangle_other | 3.918 |
r_scbond_it | 3.583 |
r_scbond_other | 3.582 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5122 |
Nucleic Acid Atoms | |
Solvent Atoms | 324 |
Heterogen Atoms | 235 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |