2G76

Crystal structure of human 3-phosphoglycerate dehydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YGYPDB ENTRY 1YGY, 1PSD
experimental modelPDB 1PSDPDB ENTRY 1YGY, 1PSD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M MMT, 30 % PEG1k, 5mM NAD+, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1643.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.084α = 90
b = 124.113β = 100.99
c = 59.502γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99806SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.736.298.96662666626
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7696.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1YGY, 1PSD1.736.26321963219337198.60.18280.180980.21644RANDOM25.461
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]
0.12-0.082-2.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.94
r_dihedral_angle_3_deg12.983
r_dihedral_angle_4_deg12.396
r_dihedral_angle_1_deg5.893
r_scangle_it2.637
r_scbond_it1.759
r_angle_refined_deg1.453
r_mcangle_it1.014
r_angle_other_deg0.932
r_mcbond_it0.709
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.94
r_dihedral_angle_3_deg12.983
r_dihedral_angle_4_deg12.396
r_dihedral_angle_1_deg5.893
r_scangle_it2.637
r_scbond_it1.759
r_angle_refined_deg1.453
r_mcangle_it1.014
r_angle_other_deg0.932
r_mcbond_it0.709
r_nbd_refined0.221
r_nbd_other0.199
r_symmetry_vdw_other0.194
r_mcbond_other0.186
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.139
r_symmetry_hbond_refined0.129
r_nbtor_other0.085
r_chiral_restr0.081
r_symmetry_vdw_refined0.046
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4413
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing