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Crystal structure of serine bound G336V,G337V double mutant of E.coli phosphoglycerate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PSD pdb entry 1PSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 291 30% PEG 400, 0.1M acetate, 0.2M Calcium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.82 56.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.072 α = 90 b = 132.239 β = 90 c = 52.37 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 IMAGE PLATE RIGAKU RAXIS IV monochromator 2006-05-09 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 2.8 40.32 99.5 0.052 20.1 3.3 25289
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 2.8 2.95 100 0.207 4.8 3.3
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 1PSD 2.8 35 23997 1285 99.2 0.20004 0.19737 0.1908 0.25008 0.2509 RANDOM 44.721
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] -3.14 -3 6.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.971 r_dihedral_angle_4_deg 23.879 r_dihedral_angle_3_deg 18.899 r_scbond_it 8.101 r_dihedral_angle_1_deg 6.421 r_mcangle_it 6.244 r_mcbond_it 4.074 r_angle_refined_deg 1.869 r_nbtor_refined 0.344 r_nbd_refined 0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.971 r_dihedral_angle_4_deg 23.879 r_dihedral_angle_3_deg 18.899 r_scbond_it 8.101 r_dihedral_angle_1_deg 6.421 r_mcangle_it 6.244 r_mcbond_it 4.074 r_angle_refined_deg 1.869 r_nbtor_refined 0.344 r_nbd_refined 0.274 r_symmetry_hbond_refined 0.261 r_xyhbond_nbd_refined 0.216 r_symmetry_vdw_refined 0.187 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6130 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction CCP4 data scaling PHASER phasing