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Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with NAD and L-Tartrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1 M Tris, pH 8.5
0.2 M MgCl2 hexahydrate
20 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.523 α = 90 b = 109.719 β = 94.4 c = 66.923 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2014-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.3 66.73 98.6 0.083 0.048 0.998 2.2 3.88 27448
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 98.5 0.627 0.511 0.812 2.2 3.85
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 2G76 2.3 66.73 26108 1319 98.5 0.2148 0.2129 0.2135 0.2548 0.2526 RANDOM 55.104
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] 3.38 0.08 0.15 -3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.98 r_dihedral_angle_4_deg 16.54 r_dihedral_angle_3_deg 15.806 r_dihedral_angle_1_deg 6.236 r_angle_refined_deg 2.217 r_angle_other_deg 1.176 r_chiral_restr 0.123 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.98 r_dihedral_angle_4_deg 16.54 r_dihedral_angle_3_deg 15.806 r_dihedral_angle_1_deg 6.236 r_angle_refined_deg 2.217 r_angle_other_deg 1.176 r_chiral_restr 0.123 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4392 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling PHASER phasing