5NZO

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 1-methyl-3-phenyl-1H-pyrazol-5-amine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M PCTP buffer, pH 7 and 23-28 % (w/v) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.2745.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.391α = 97.05
b = 45.783β = 110.12
c = 54.807γ = 106.65
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2014-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.920DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.2949.982.80.09141.9473976
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.311.3384.20.9170.3521.93742

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 REPLACEMENTTHROUGHOUT2G761.2949.8870307365179.110.19840.19630.2406RANDOM20.254
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]
-0.120.79-0.2-0.21.68-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.383
r_dihedral_angle_2_deg36.619
r_sphericity_bonded19.943
r_dihedral_angle_4_deg16.725
r_dihedral_angle_3_deg14.362
r_dihedral_angle_1_deg6.804
r_rigid_bond_restr4.261
r_angle_refined_deg1.962
r_angle_other_deg1.467
r_chiral_restr0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.383
r_dihedral_angle_2_deg36.619
r_sphericity_bonded19.943
r_dihedral_angle_4_deg16.725
r_dihedral_angle_3_deg14.362
r_dihedral_angle_1_deg6.804
r_rigid_bond_restr4.261
r_angle_refined_deg1.962
r_angle_other_deg1.467
r_chiral_restr0.132
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.008
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2920
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms26

Software

Software
Software NamePurpose
xia2data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing