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Crystal structure of Cag VirB11 (HP0525) and an inhibitory protein (HP1451)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G6O PDB ENTRY 1G6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 100mM Mes, 8% polyethylene glycol 8,000, 10mM ethylene-diamine-tetra-acetic acid, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.65 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.851 α = 111.04 b = 86.9 β = 95.98 c = 104.129 γ = 104.94
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2006-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97590 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 94.916 96.3 0.091 0.091 5 3.3 104768 100842 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 96.5 0.243 0.243 2.9 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1G6O 2.4 40 104768 95786 5056 96.27 0.23185 0.22986 0.2294 0.26966 0.2682 RANDOM 33.827
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] -0.49 -0.01 0.26 0.45 0.1 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.172 r_dihedral_angle_4_deg 17.29 r_dihedral_angle_3_deg 16.584 r_dihedral_angle_1_deg 5.609 r_scangle_it 1.643 r_angle_refined_deg 1.197 r_scbond_it 0.999 r_mcangle_it 0.92 r_mcbond_it 0.589 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.172 r_dihedral_angle_4_deg 17.29 r_dihedral_angle_3_deg 16.584 r_dihedral_angle_1_deg 5.609 r_scangle_it 1.643 r_angle_refined_deg 1.197 r_scbond_it 0.999 r_mcangle_it 0.92 r_mcbond_it 0.589 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.194 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17207 Nucleic Acid Atoms Solvent Atoms 687 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction