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Sporosarcina pasteurii urease in complex with a hydrophilic derivative of Ebsulfur at 1.96 A
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 6.3 293 1.7-2.1 M ammonium sulfate, 100 mM citrate, pH 6.3
Crystal Properties Matthews coefficient Solvent content 2.74 55.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.202 α = 90 b = 131.202 β = 90 c = 188.949 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 EIGER X 16M 2024-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 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 1.96 48.69 100 0.17 0.181 0.043 0.999 12.8 16.9 69291 28.53
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 1.96 2 100 1.827 1.935 0.461 0.809 1.5 17.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.96 48.73 65874 3373 99.93 0.14151 0.13957 0.1527 0.17843 0.1885 RANDOM 35.398
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] 1.32 0.66 1.32 -4.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.653 r_dihedral_angle_4_deg 18.279 r_dihedral_angle_3_deg 13.486 r_dihedral_angle_1_deg 7.382 r_long_range_B_other 6.448 r_long_range_B_refined 6.447 r_scangle_other 5.152 r_scbond_it 3.662 r_scbond_other 3.662 r_mcangle_it 3.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.653 r_dihedral_angle_4_deg 18.279 r_dihedral_angle_3_deg 13.486 r_dihedral_angle_1_deg 7.382 r_long_range_B_other 6.448 r_long_range_B_refined 6.447 r_scangle_other 5.152 r_scbond_it 3.662 r_scbond_other 3.662 r_mcangle_it 3.198 r_mcangle_other 3.198 r_mcbond_it 2.387 r_mcbond_other 2.385 r_angle_refined_deg 1.632 r_angle_other_deg 1.363 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6045 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 231
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing