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Crystal structure of YopR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 20% (w/v) PEG 8000, 100 mM Sodium phosphate dibasic/ Citric acid pH 4.2, 200 mM Sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.43 49.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.682 α = 90 b = 108.007 β = 90.36 c = 53.601 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 2021-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9718 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 2.6 94.84 98.2 0.095 0.037 0.998 12.5 6.4 32678
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) 2.6 2.74 94.5 0.46 0.194 0.933 5.8
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 SAD THROUGHOUT 2.6 94.84 30962 1634 97.85 0.21977 0.21789 0.2245 0.2545 0.2579 RANDOM 66.128
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] -1.91 -0.21 4.12 -2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.696 r_dihedral_angle_4_deg 24.328 r_dihedral_angle_3_deg 18.348 r_dihedral_angle_1_deg 5.778 r_long_range_B_refined 5.277 r_long_range_B_other 5.276 r_mcangle_it 3.384 r_mcangle_other 3.384 r_scangle_other 3.342 r_mcbond_it 1.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.696 r_dihedral_angle_4_deg 24.328 r_dihedral_angle_3_deg 18.348 r_dihedral_angle_1_deg 5.778 r_long_range_B_refined 5.277 r_long_range_B_other 5.276 r_mcangle_it 3.384 r_mcangle_other 3.384 r_scangle_other 3.342 r_mcbond_it 1.968 r_mcbond_other 1.967 r_scbond_it 1.946 r_scbond_other 1.946 r_angle_refined_deg 1.518 r_angle_other_deg 1.005 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 7802 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement XDS data reduction CRANK2 phasing