5N6C

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with NAD and L-Tartrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G76 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.1 M Tris, pH 8.5 0.2 M MgCl2 hexahydrate 20 % (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4850.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.523α = 90
b = 109.719β = 94.4
c = 66.923γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2014-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.366.7398.60.0830.0480.9982.23.8827448
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3898.50.6270.5110.8122.23.85

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2G762.366.7326108131998.50.21480.21290.2548RANDOM55.104
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]
3.380.080.15-3.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.98
r_dihedral_angle_4_deg16.54
r_dihedral_angle_3_deg15.806
r_dihedral_angle_1_deg6.236
r_angle_refined_deg2.217
r_angle_other_deg1.176
r_chiral_restr0.123
r_bond_refined_d0.024
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.98
r_dihedral_angle_4_deg16.54
r_dihedral_angle_3_deg15.806
r_dihedral_angle_1_deg6.236
r_angle_refined_deg2.217
r_angle_other_deg1.176
r_chiral_restr0.123
r_bond_refined_d0.024
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4392
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing