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Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-fluoro-2-methylbenzoic acid
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 2.01 38.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.342 α = 98.02 b = 45.608 β = 111.14 c = 56.269 γ = 105.85
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 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.979 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 1.5 50.6 91.4 0.084 0.076 0.977 5 1.93 54400
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 90.1 1.241 1.141 0.598 1.85
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 50.6 51322 2775 89.5 0.22618 0.22366 0.2264 0.27266 0.2712 RANDOM 19.256
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] -0.42 0.1 0.28 -0.33 0.69 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.6 r_sphericity_free 34.648 r_dihedral_angle_3_deg 16.524 r_sphericity_bonded 16.444 r_dihedral_angle_4_deg 14.792 r_dihedral_angle_1_deg 7.579 r_rigid_bond_restr 6.58 r_long_range_B_refined 5.079 r_long_range_B_other 5.079 r_scangle_other 4.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.6 r_sphericity_free 34.648 r_dihedral_angle_3_deg 16.524 r_sphericity_bonded 16.444 r_dihedral_angle_4_deg 14.792 r_dihedral_angle_1_deg 7.579 r_rigid_bond_restr 6.58 r_long_range_B_refined 5.079 r_long_range_B_other 5.079 r_scangle_other 4.901 r_scbond_it 4.176 r_scbond_other 4.153 r_mcangle_it 3.953 r_mcangle_other 3.953 r_mcbond_it 3.523 r_mcbond_other 3.506 r_angle_refined_deg 2.296 r_angle_other_deg 1.566 r_chiral_restr 0.154 r_bond_refined_d 0.025 r_gen_planes_refined 0.014 r_bond_other_d 0.009 r_gen_planes_other 0.006 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 275 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing