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Human OMPD-domain of UMPS in complex with substrate OMP at 1.05 Angstroms resolution, 20 minutes soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293.15 Ammonium sulfate, Tris/HCl, Glutathion, Glycerol
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.964 α = 90 b = 61.882 β = 113.09 c = 70.052 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 PIXEL DECTRIS EIGER X 16M 2018-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.827 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.05 42.51 97.2 0.05 0.059 0.999 12.35 3.491 248705 12.916
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.08 93.3 0.8 0.963 0.661 1.7 3.19
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 6ZWY 1.05 42.51 236444 12264 97.31 0.1216 0.121 0.121 0.1336 0.1334 RANDOM 13.795
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] 0.18 0.57 -0.97 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.966 r_dihedral_angle_4_deg 16.092 r_dihedral_angle_3_deg 12.904 r_dihedral_angle_1_deg 6.73 r_angle_other_deg 1.525 r_angle_refined_deg 1.468 r_rigid_bond_restr 0.884 r_chiral_restr 0.08 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.966 r_dihedral_angle_4_deg 16.092 r_dihedral_angle_3_deg 12.904 r_dihedral_angle_1_deg 6.73 r_angle_other_deg 1.525 r_angle_refined_deg 1.468 r_rigid_bond_restr 0.884 r_chiral_restr 0.08 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3923 Nucleic Acid Atoms Solvent Atoms 712 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction