☰ Navigation Tabs
1.63 A resolution hydroquinone inhibited Sporosarcina pasteurii urease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G4H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 THE PROTEIN-LIGAND (1 mM) COMPLEX IN 50 MM HEPES BUFFER, PH 7.50, DILUTED 1:1 WITH A SOLUTION OF 1.6-2.0 M AMMONIUM SULFATE in 100 mM citrate buffer at pH 6.3
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.666 α = 90 b = 131.666 β = 90 c = 189.129 γ = 120
Symmetry Space Group P 63 2 2
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 PILATUS 6M-F 2022-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9537 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.63 115 100 0.12 0.127 0.043 19.9 16.3 120118
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.66 100 1.99 2.142 0.786 1.5 14.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5G4H 1.63 114.287 120090 5968 99.864 0.129 0.1279 0.1427 0.158 0.1689 22.827
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] 0.68 0.34 0.68 -2.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.016 r_dihedral_angle_4_deg 18.179 r_dihedral_angle_3_deg 12.492 r_dihedral_angle_other_3_deg 11.858 r_lrange_it 7.294 r_lrange_other 7.151 r_dihedral_angle_1_deg 6.92 r_scangle_it 4.886 r_scangle_other 4.487 r_scbond_it 3.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.016 r_dihedral_angle_4_deg 18.179 r_dihedral_angle_3_deg 12.492 r_dihedral_angle_other_3_deg 11.858 r_lrange_it 7.294 r_lrange_other 7.151 r_dihedral_angle_1_deg 6.92 r_scangle_it 4.886 r_scangle_other 4.487 r_scbond_it 3.392 r_scbond_other 3.059 r_mcangle_other 2.297 r_mcangle_it 2.296 r_angle_refined_deg 1.851 r_mcbond_it 1.685 r_mcbond_other 1.682 r_angle_other_deg 1.5 r_nbd_refined 0.237 r_nbd_other 0.226 r_symmetry_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.21 r_symmetry_nbd_other 0.181 r_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.163 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.077 r_xyhbond_nbd_other 0.035 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6046 Nucleic Acid Atoms Solvent Atoms 667 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing