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H-PGDS complexed with inhibitor 1Y
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6N4E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 50mM Tris(hydroxymethyl)aminomethane hydrochloride pH 7.5, 50 mM sodium chloride, 1mM DTT, 15 mM glutathione, 1 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.331 α = 90 b = 67.197 β = 96.88 c = 69.74 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 CCD MARRESEARCH 2017-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.96 100 95.2 0.054 0.062 0.03 23.66 3.9 29980
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 1.99 73 0.648 2.4
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 6N4E 1.97 47.98 22351 1171 74.51 0.1998 0.1977 0.2038 0.2388 0.2445 RANDOM 32.436
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] 0.02 -0.05 -0.28 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.644 r_dihedral_angle_4_deg 19.06 r_dihedral_angle_3_deg 13.291 r_dihedral_angle_1_deg 5.247 r_angle_other_deg 1.654 r_angle_refined_deg 1.408 r_chiral_restr 0.094 r_bond_other_d 0.018 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.644 r_dihedral_angle_4_deg 19.06 r_dihedral_angle_3_deg 13.291 r_dihedral_angle_1_deg 5.247 r_angle_other_deg 1.654 r_angle_refined_deg 1.408 r_chiral_restr 0.094 r_bond_other_d 0.018 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3194 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing