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Virulence-associated protein VapG from the intracellular pathogen Rhodococcus equi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CSB PDB ENTRY 4CSB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN SOLUTION: 30 MG/ML VAPG IN 10 MM TRIS-HCL PH 7.5, 10 MM NACL RESERVOIR: 0.3 M KCL, 20 % W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.72 29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.55 α = 90 b = 44.55 β = 90 c = 259.67 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PIXEL MIRRORS 2013-03-17 M SINGLE WAVELENGTH
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 1.8 31.5 98 0.04 31 11.4 24979
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 1.8 1.85 83 0.67 2.6 7.2
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 PDB ENTRY 4CSB 1.8 31.5 23612 1267 97.87 0.20094 0.1991 0.2084 0.23623 0.2431 RANDOM 31.009
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] -0.12 -0.12 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.433 r_dihedral_angle_3_deg 12.647 r_dihedral_angle_1_deg 6.449 r_mcangle_it 3.982 r_scbond_it 3.718 r_mcbond_it 3.101 r_mcbond_other 3.069 r_angle_refined_deg 1.893 r_angle_other_deg 0.895 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.433 r_dihedral_angle_3_deg 12.647 r_dihedral_angle_1_deg 6.449 r_mcangle_it 3.982 r_scbond_it 3.718 r_mcbond_it 3.101 r_mcbond_other 3.069 r_angle_refined_deg 1.893 r_angle_other_deg 0.895 r_chiral_restr 0.126 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.001 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 1611 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction XDS data scaling MOLREP phasing