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Crystal structure of extragenic suppressor protein suhB from Bartonella henselae, native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 24 mg/mL protein against 0.2M MgCl2, 0.1 M Tris pH 8.5, 30% PEG 400, crystal tracking ID 205526c1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.24 62.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.06 α = 90 b = 138.6 β = 90 c = 67.24 γ = 90
Symmetry Space Group P 21 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 210r 2010-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 1.85 70.61 99.8 0.061 19.58 7.9 66080 -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) 1.85 1.9 99.2 0.552 3.5 6.7
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 3LUZ 1.85 30 62729 3351 99.75 0.19257 0.19122 0.1897 0.21816 0.218 RANDOM 27.973
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] -0.43 0.99 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.552 r_dihedral_angle_4_deg 15.195 r_dihedral_angle_3_deg 13.87 r_dihedral_angle_1_deg 6.11 r_scangle_it 4.365 r_scbond_it 2.562 r_mcangle_it 1.575 r_angle_refined_deg 1.434 r_mcbond_it 0.856 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.552 r_dihedral_angle_4_deg 15.195 r_dihedral_angle_3_deg 13.87 r_dihedral_angle_1_deg 6.11 r_scangle_it 4.365 r_scbond_it 2.562 r_mcangle_it 1.575 r_angle_refined_deg 1.434 r_mcbond_it 0.856 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4072 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 3
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction