2P9E

Crystal Structure of G336V mutant of E.coli phosphoglycerate dehydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PA3PDB entry 2PA3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52911.5M AmSO4, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.957.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.237α = 90
b = 76.237β = 90
c = 353.65γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Monochromator2005-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

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
12.65099.50.16519.318.761423
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.6996.10.8461.6410.8

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 REPLACEMENTTHROUGHOUTPDB entry 2PA32.63558183310599.540.20980.20610.27923RANDOM40.904
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]
2.272.27-4.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.626
r_dihedral_angle_3_deg21.398
r_dihedral_angle_4_deg21.238
r_scangle_it10.225
r_scbond_it8.023
r_dihedral_angle_1_deg6.839
r_mcangle_it5.998
r_mcbond_it4.03
r_angle_refined_deg1.92
r_symmetry_hbond_refined0.434
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.626
r_dihedral_angle_3_deg21.398
r_dihedral_angle_4_deg21.238
r_scangle_it10.225
r_scbond_it8.023
r_dihedral_angle_1_deg6.839
r_mcangle_it5.998
r_mcbond_it4.03
r_angle_refined_deg1.92
r_symmetry_hbond_refined0.434
r_nbtor_refined0.342
r_nbd_refined0.281
r_symmetry_vdw_refined0.232
r_xyhbond_nbd_refined0.221
r_chiral_restr0.121
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12267
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms299

Software

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