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Crystal structure of a single strand binding protein (SSB) from bartonella henselae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LGJ PDB ENTRY 3lGJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 290 25 % PEG 3350, 200 MM NACL, 100 MM TRIS HCL, PROTEIN AT 4.5 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 9.0
Crystal Properties Matthews coefficient Solvent content 1.86 33.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.76 α = 90 b = 93.76 β = 90 c = 63.51 γ = 120
Symmetry Space Group P 32 2 1
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 RIGAKU SATURN 944+ 2010-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.1 50 98.7 0.061 22.67 6.7 19153 18898 -3 35.73
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) 2.1 2.15 96 0.527 3.2 5 1386
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 (All) 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 3lGJ 2.1 46.88 18898 18828 972 98.4 0.212 0.212 0.21 0.2125 0.256 0.2611 RANDOM 25.14
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] -0.14 -0.07 -0.14 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.649 r_dihedral_angle_4_deg 22.153 r_dihedral_angle_3_deg 14.716 r_dihedral_angle_1_deg 6.164 r_scangle_it 4.387 r_scbond_it 2.578 r_mcangle_it 1.639 r_angle_refined_deg 1.596 r_angle_other_deg 0.859 r_mcbond_it 0.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.649 r_dihedral_angle_4_deg 22.153 r_dihedral_angle_3_deg 14.716 r_dihedral_angle_1_deg 6.164 r_scangle_it 4.387 r_scbond_it 2.578 r_mcangle_it 1.639 r_angle_refined_deg 1.596 r_angle_other_deg 0.859 r_mcbond_it 0.838 r_mcbond_other 0.176 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1804 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 6
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling