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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 1PSD pdb entry 1PSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 291 20% PEG1000, 0.1M Na/K phosphate, 0.2M MgCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.789 α = 90 b = 152.789 β = 90 c = 163.66 γ = 120
Symmetry Space Group P 62 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 monochromator 2005-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9795 APS 23-ID-B
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 2.74 50 99.9 0.081 39.78 20.4 30270
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 2.74 2.84 99.8 0.594 5.23 16.4
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 2.74 35 28694 1528 99.93 0.2188 0.21703 0.2168 0.25336 0.2511 RANDOM 64.607
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] 1.08 0.54 1.08 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.823 r_dihedral_angle_4_deg 25.788 r_dihedral_angle_3_deg 21.634 r_scangle_it 10.015 r_scbond_it 7.734 r_dihedral_angle_1_deg 6.064 r_mcangle_it 5.947 r_mcbond_it 3.989 r_angle_refined_deg 1.811 r_nbtor_refined 0.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.823 r_dihedral_angle_4_deg 25.788 r_dihedral_angle_3_deg 21.634 r_scangle_it 10.015 r_scbond_it 7.734 r_dihedral_angle_1_deg 6.064 r_mcangle_it 5.947 r_mcbond_it 3.989 r_angle_refined_deg 1.811 r_nbtor_refined 0.345 r_symmetry_hbond_refined 0.337 r_nbd_refined 0.269 r_symmetry_vdw_refined 0.243 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 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 3076 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing