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Crystal structure of YopR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BJV 8BJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 30.00 % w/v Polyethylene glycol 4,000, 100 mM tri-Sodium citrate; pH 5.6, 100 mM Ammonium sulfate3/D
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.081 α = 90 b = 109.081 β = 90 c = 53.908 γ = 120
Symmetry Space Group P 3 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 2021-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97934 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 94.47 100 0.077 0.018 0.999 23 18.9 19078
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 2.32 100 0.445 0.099 0.985 20.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8BJV 2.2 94.47 17599 1479 99.99 0.19967 0.19547 0.24861 0.2787 RANDOM 60.647
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] 0.42 0.21 0.42 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.583 r_sphericity_bonded 28.398 r_dihedral_angle_4_deg 22.227 r_dihedral_angle_3_deg 17.676 r_dihedral_angle_1_deg 5.734 r_scangle_other 5.467 r_long_range_B_refined 5.403 r_long_range_B_other 5.377 r_scbond_other 5.129 r_scbond_it 5.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.583 r_sphericity_bonded 28.398 r_dihedral_angle_4_deg 22.227 r_dihedral_angle_3_deg 17.676 r_dihedral_angle_1_deg 5.734 r_scangle_other 5.467 r_long_range_B_refined 5.403 r_long_range_B_other 5.377 r_scbond_other 5.129 r_scbond_it 5.115 r_mcangle_other 4.846 r_mcangle_it 4.833 r_rigid_bond_restr 4.336 r_mcbond_it 4.092 r_mcbond_other 4.068 r_angle_other_deg 3.73 r_angle_refined_deg 1.406 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2608 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement XDS data reduction MOLREP phasing