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Crystal structure of Rhodococcus equi VapB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 SITTING DROP VAPOUR DIFFUSION AT 293 K WITH 1 UL PROTEIN (10 MG/ML) PLUS 0.5 UL RESERVOIR SOLUTION CONSISTING OF 0.01 M COCL2, 0.1 M NA-ACETATE, PH 4.6, AND 1.0 M HEXANEDIOL (JCSG CORE II CONDITION G4).
Crystal Properties Matthews coefficient Solvent content 2.79 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.82 α = 90 b = 83.82 β = 90 c = 49.13 γ = 120
Symmetry Space Group P 61 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 2012-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 50 100 0.1 26.9 37 20584 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 100 1.26 2.67 29
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 1.4 50 18526 2030 99.95 0.17252 0.16972 0.1797 0.19854 0.2071 RANDOM 20.913
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] 0.29 0.14 0.29 -0.92
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.234 r_mcangle_it 1.675 r_scbond_it 1.618 r_mcbond_it 1.141 r_mcbond_other 1.139 r_angle_other_deg 1.039 r_chiral_restr 0.155 r_bond_refined_d 0.024 r_gen_planes_refined 0.015 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.234 r_mcangle_it 1.675 r_scbond_it 1.618 r_mcbond_it 1.141 r_mcbond_other 1.139 r_angle_other_deg 1.039 r_chiral_restr 0.155 r_bond_refined_d 0.024 r_gen_planes_refined 0.015 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 840 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELXD phasing