5YVT
Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and NADH
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5GRH |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.1 M HEPES-Na, pH 7.5, 50 mM MgCl2, 30% (v/v) PEGMME 550 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.78 | 67.48 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 118.027 | α = 90 |
b = 118.027 | β = 90 |
c = 142.109 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2017-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.9785 | SSRF | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.4 | 50 | 100 | 22.6 | 9.9 | 45428 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.4 | 2.49 | 100 | 2.8 | 8.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5GRH | 2.4 | 50 | 43063 | 2323 | 99.93 | 0.2126 | 0.21136 | 0.23637 | RANDOM | 64.145 |
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] | |
1.4 | 0.7 | 1.4 | -4.53 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.998 |
r_dihedral_angle_4_deg | 23.149 |
r_dihedral_angle_3_deg | 15.806 |
r_long_range_B_refined | 6.281 |
r_dihedral_angle_1_deg | 5.502 |
r_mcangle_it | 3.165 |
r_scbond_it | 2.246 |
r_mcbond_it | 1.856 |
r_angle_refined_deg | 1.296 |
r_chiral_restr | 0.08 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5048 |
Nucleic Acid Atoms | |
Solvent Atoms | 94 |
Heterogen Atoms | 89 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
PHASER | phasing |