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Crystal structure of YopR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B6J 8B6J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 20 % w/v Polyethylene glycol 6,000 100 mM tri-Sodium citrate; pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.35 47.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.912 α = 90 b = 107.75 β = 90.8 c = 52.87 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2022-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 93.22 95.6 0.077 0.03 0.999 13.8 6.1 50520
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.32 75.6 0.648 0.323 0.816 3.8
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 8B6J 2.2 93.22 46857 3659 95.55 0.21899 0.21613 0.2184 0.25437 0.2525 RANDOM 51.751
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] 0.3 0.74 0.78 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.2 r_dihedral_angle_4_deg 22.408 r_dihedral_angle_3_deg 17.044 r_dihedral_angle_1_deg 5.69 r_long_range_B_refined 5.446 r_long_range_B_other 5.446 r_scangle_other 3.639 r_mcangle_it 3.337 r_mcangle_other 3.337 r_scbond_it 2.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.2 r_dihedral_angle_4_deg 22.408 r_dihedral_angle_3_deg 17.044 r_dihedral_angle_1_deg 5.69 r_long_range_B_refined 5.446 r_long_range_B_other 5.446 r_scangle_other 3.639 r_mcangle_it 3.337 r_mcangle_other 3.337 r_scbond_it 2.147 r_scbond_other 2.145 r_mcbond_it 2.054 r_mcbond_other 2.052 r_angle_refined_deg 1.472 r_angle_other_deg 0.969 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 7807 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 18
Software Software Software Name Purpose SCALA data scaling REFMAC refinement XDS data reduction MOLREP phasing