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Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with N-(3-chloro-4-methoxyphenyl) acetamide
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 7 298 0.1 M PCTP, pH 7, 23-25 % PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.26 45.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.353 α = 97.9 b = 45.323 β = 110.06 c = 55.255 γ = 106.35
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 2014-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.48 50.12 86.1 0.111 0.1 4.6 2.13 51238
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 1.5 1.53 85.8 1.088 0.972 0.355 0.9 2.14
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 1.48 50.12 48587 2651 84.57 0.1919 0.1891 0.1892 0.2435 0.2387 RANDOM 19.681
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] -0.04 -0.47 0.68 -0.58 1.25 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.191 r_sphericity_free 36.748 r_sphericity_bonded 21.853 r_dihedral_angle_4_deg 20.453 r_dihedral_angle_3_deg 17.769 r_dihedral_angle_1_deg 6.947 r_rigid_bond_restr 4.372 r_angle_refined_deg 1.978 r_angle_other_deg 1.412 r_chiral_restr 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.191 r_sphericity_free 36.748 r_sphericity_bonded 21.853 r_dihedral_angle_4_deg 20.453 r_dihedral_angle_3_deg 17.769 r_dihedral_angle_1_deg 6.947 r_rigid_bond_restr 4.372 r_angle_refined_deg 1.978 r_angle_other_deg 1.412 r_chiral_restr 0.123 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2920 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing