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X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)Cl determined at 1.72 Angstroms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 THE PROTEIN-LIGAND (300 microM) COMPLEX IN 50 mM
HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO),
DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE
ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO.
Crystal Properties Matthews coefficient Solvent content 2.76 55.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.441 α = 90 b = 131.441 β = 90 c = 189.759 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 2019-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 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) 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 1.72 189.76 100 0.134 0.141 0.044 1 19.3 19.6 102636 27.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 99.9 4.03 4.235 1.297 0.699 1 20.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6G48 1.72 72.989 102502 5112 99.904 0.157 0.1555 0.1683 0.1852 0.1979 random 31.389
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] 1.082 0.541 1.082 -3.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 17.41 r_dihedral_angle_3_deg 13.371 r_lrange_it 7.82 r_lrange_other 7.454 r_dihedral_angle_1_deg 7.359 r_scangle_it 5.429 r_scangle_other 4.622 r_scbond_it 3.827 r_scbond_other 3.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.301 r_dihedral_angle_4_deg 17.41 r_dihedral_angle_3_deg 13.371 r_lrange_it 7.82 r_lrange_other 7.454 r_dihedral_angle_1_deg 7.359 r_scangle_it 5.429 r_scangle_other 4.622 r_scbond_it 3.827 r_scbond_other 3.323 r_mcangle_it 2.649 r_mcangle_other 2.649 r_mcbond_it 2.184 r_mcbond_other 2.182 r_angle_refined_deg 1.708 r_angle_other_deg 1.424 r_symmetry_nbd_refined 0.236 r_nbd_refined 0.206 r_symmetry_xyhbond_nbd_refined 0.186 r_nbd_other 0.183 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6047 Nucleic Acid Atoms Solvent Atoms 621 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing