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Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole
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 2.02 39.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.342 α = 97.91 b = 45.86 β = 110.74 c = 56.175 γ = 106.39
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) 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 50.66 86.4 0.064 0.058 0.99 6.3 2.1 51430
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 86.3 0.376 0.344 0.804 2
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 50.66 48623 2653 84.73 0.19415 0.19118 0.2 0.24917 0.2598 RANDOM 15.757
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] 0.27 0.19 -0.7 -0.76 -0.18 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.676 r_sphericity_free 32.417 r_dihedral_angle_4_deg 20.688 r_dihedral_angle_3_deg 17.043 r_sphericity_bonded 12.662 r_dihedral_angle_1_deg 7.035 r_long_range_B_refined 4.591 r_long_range_B_other 4.591 r_scangle_other 3.718 r_scbond_it 3.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.676 r_sphericity_free 32.417 r_dihedral_angle_4_deg 20.688 r_dihedral_angle_3_deg 17.043 r_sphericity_bonded 12.662 r_dihedral_angle_1_deg 7.035 r_long_range_B_refined 4.591 r_long_range_B_other 4.591 r_scangle_other 3.718 r_scbond_it 3.274 r_scbond_other 3.274 r_mcangle_it 3.259 r_mcangle_other 3.259 r_rigid_bond_restr 3.158 r_mcbond_it 2.874 r_mcbond_other 2.462 r_angle_refined_deg 2.155 r_angle_other_deg 1.157 r_chiral_restr 0.139 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 305 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing