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Crystal structure of serine bound G336V mutant of E.coli phosphoglycerate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PA3 PDB entry 2PA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 10% PEG3000, 0.1M cacodylate, 0.2M MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.63 53.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.142 α = 90 b = 130.785 β = 90 c = 50.188 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2006-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.46 35 88.7 0.096 20.2 7.6 31001
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.59 72.2 0.544 2.5 8.2 3604
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2PA3 2.46 35 29392 1556 88.62 0.22204 0.21894 0.2172 0.28059 0.2793 RANDOM 45.721
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] -1.57 -2.76 4.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.95 r_dihedral_angle_4_deg 20.187 r_dihedral_angle_3_deg 18.637 r_scangle_it 7.547 r_scbond_it 5.942 r_dihedral_angle_1_deg 5.881 r_mcangle_it 4.389 r_mcbond_it 2.9 r_angle_refined_deg 1.394 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.95 r_dihedral_angle_4_deg 20.187 r_dihedral_angle_3_deg 18.637 r_scangle_it 7.547 r_scbond_it 5.942 r_dihedral_angle_1_deg 5.881 r_mcangle_it 4.389 r_mcbond_it 2.9 r_angle_refined_deg 1.394 r_nbtor_refined 0.328 r_symmetry_hbond_refined 0.326 r_nbd_refined 0.255 r_symmetry_vdw_refined 0.214 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6140 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction CCP4 data scaling PHASER phasing