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Structure of the Virulence-Associated Protein VapD from the intracellular pathogen Rhodococcus equi.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 PROTEIN:20 MG ML-1 VAPD-CORE IN 20 MM HEPES PH 7.5, 500 MM NACL RESERVOIR: 2.2M AMMONIUM SULPHATE, 0.2M SODIUM THIOCYANATE, 0.1% WV-1 BETA-D-OCTYL GLUCOSIDE
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.844 α = 90 b = 142.844 β = 90 c = 142.844 γ = 90
Symmetry Space Group F 4 3 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 MIRRORS 2013-03-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.9 82.5 100 0.09 21 11.9 10376
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 1.9 1.94 100 0.83 3.7 12
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 SAD THROUGHOUT NONE 1.9 82.47 9823 497 99.54 0.16077 0.15923 0.19078 0.1782 RANDOM 28.742
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.302 r_dihedral_angle_3_deg 15.025 r_dihedral_angle_4_deg 8.236 r_dihedral_angle_1_deg 6.326 r_mcangle_it 4.283 r_scbond_it 4.231 r_mcbond_it 2.968 r_mcbond_other 2.881 r_angle_refined_deg 2.141 r_angle_other_deg 1.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.302 r_dihedral_angle_3_deg 15.025 r_dihedral_angle_4_deg 8.236 r_dihedral_angle_1_deg 6.326 r_mcangle_it 4.283 r_scbond_it 4.231 r_mcbond_it 2.968 r_mcbond_other 2.881 r_angle_refined_deg 2.141 r_angle_other_deg 1.711 r_chiral_restr 0.224 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.001 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 857 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling SHELX phasing