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Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-(1,3-oxazol-5-yl)aniline.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M PCTP pH 7, 23-25 % PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.02 39.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.335 α = 97.85 b = 45.914 β = 111.05 c = 56.203 γ = 106.04
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 2014-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.917 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 50.61 86.3 0.986 4.7 2.15 51377
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 86.9 0.585
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.5 50.61 48604 2653 84.48 0.23148 0.22811 0.2222 0.29307 0.2895 RANDOM 21.983
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] -0.79 1.1 0.37 -0.52 1.34 -0.47
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.87 r_dihedral_angle_2_deg 38.528 r_dihedral_angle_4_deg 20.254 r_sphericity_bonded 20.11 r_dihedral_angle_3_deg 16.689 r_long_range_B_refined 7.085 r_long_range_B_other 7.084 r_dihedral_angle_1_deg 6.955 r_scangle_other 5.694 r_mcangle_other 5.347
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.87 r_dihedral_angle_2_deg 38.528 r_dihedral_angle_4_deg 20.254 r_sphericity_bonded 20.11 r_dihedral_angle_3_deg 16.689 r_long_range_B_refined 7.085 r_long_range_B_other 7.084 r_dihedral_angle_1_deg 6.955 r_scangle_other 5.694 r_mcangle_other 5.347 r_mcangle_it 5.331 r_scbond_it 4.945 r_scbond_other 4.945 r_mcbond_it 4.547 r_mcbond_other 4.472 r_rigid_bond_restr 3.572 r_angle_refined_deg 2.051 r_angle_other_deg 1.393 r_chiral_restr 0.131 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2920 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing