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Crystal structure of the soluble domain of VirB8 from Bartonella grahamii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 BagrA.18388.a.B2.PW37031 at 6.35 mg/mL against MCSG1 screen condition E6, 0.2 M potassium sulfate, 20% PEG 3350 with 15% ethylene glycol as cryo-protectant; crystal tracking ID 238817e6, unique puck ID acy5-8, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.73 55.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.62 α = 90 b = 60.62 β = 90 c = 124.57 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 100 CCD ADSC QUANTUM 315r 2013-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 2.55 50 99.6 0.03 42.96 6.6 8095 8063 -3 66.526
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 2.55 2.62 99.7 0.506 3.82
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 4jf8 2.55 35.34 8063 369 99.62 0.2051 0.203 0.2073 0.2491 0.2596 RANDOM 65.4664
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] -0.89 -0.89 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.246 r_dihedral_angle_3_deg 16.808 r_dihedral_angle_4_deg 13.424 r_dihedral_angle_1_deg 5.931 r_mcangle_it 4.289 r_mcbond_it 2.786 r_mcbond_other 2.768 r_angle_refined_deg 1.346 r_angle_other_deg 0.758 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.246 r_dihedral_angle_3_deg 16.808 r_dihedral_angle_4_deg 13.424 r_dihedral_angle_1_deg 5.931 r_mcangle_it 4.289 r_mcbond_it 2.786 r_mcbond_other 2.768 r_angle_refined_deg 1.346 r_angle_other_deg 0.758 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction