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X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)2NO3 determined at 1.97 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 2.74 55.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.485 α = 90 b = 131.485 β = 90 c = 189.523 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 1.97 113.87 100 0.2 0.234 0.064 0.998 12.2 13.2 68762 29.2
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 1.97 2.02 99.9 3.191 3.473 0.982 0.593 1 12.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6G48 1.97 97.798 68710 3343 99.953 0.169 0.1668 0.1784 0.2092 0.2161 37.581
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] 1.569 0.784 1.569 -5.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.793 r_dihedral_angle_4_deg 17.73 r_dihedral_angle_3_deg 14.512 r_dihedral_angle_1_deg 7.705 r_lrange_it 6.794 r_lrange_other 6.685 r_scangle_it 5.736 r_scangle_other 5.283 r_scbond_it 4.111 r_scbond_other 3.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.793 r_dihedral_angle_4_deg 17.73 r_dihedral_angle_3_deg 14.512 r_dihedral_angle_1_deg 7.705 r_lrange_it 6.794 r_lrange_other 6.685 r_scangle_it 5.736 r_scangle_other 5.283 r_scbond_it 4.111 r_scbond_other 3.819 r_mcangle_it 3.664 r_mcangle_other 3.664 r_mcbond_it 2.882 r_mcbond_other 2.881 r_angle_refined_deg 1.756 r_angle_other_deg 1.386 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.206 r_nbd_other 0.196 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_other 0.116 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6047 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing