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Crystal structure of a putative dna binding protein (bt_1116) from bacteroides thetaiotaomicron vpi-5482 at 1.50 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 277 34.0000% polyethylene glycol 400, 0.2000M lithium sulfate, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.53 51.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.688 α = 90 b = 90.688 β = 90 c = 53.888 γ = 120
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 MARMOSAIC 325 mm CCD FLAT MIRROR (VERTICAL FOCUSING) 2009-02-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97908,0.97840 SSRL BL11-1
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 1.5 29.683 97.1 0.048 10.56 3.77 79258 -3 16.81
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 1.5 1.55 95.2 0.552 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.5 29.68 79234 3974 99.8 0.145 0.143 0.167 0.1925 RANDOM 21.75
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] 0.02 0.01 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.897 r_dihedral_angle_4_deg 13.132 r_dihedral_angle_3_deg 9.688 r_dihedral_angle_1_deg 5.308 r_scangle_it 5.051 r_scbond_it 3.678 r_mcangle_it 2.354 r_mcbond_it 1.702 r_angle_refined_deg 1.584 r_angle_other_deg 1.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.897 r_dihedral_angle_4_deg 13.132 r_dihedral_angle_3_deg 9.688 r_dihedral_angle_1_deg 5.308 r_scangle_it 5.051 r_scbond_it 3.678 r_mcangle_it 2.354 r_mcbond_it 1.702 r_angle_refined_deg 1.584 r_angle_other_deg 1.134 r_mcbond_other 0.418 r_symmetry_vdw_other 0.24 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.2 r_nbd_other 0.177 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.164 r_metal_ion_refined 0.153 r_nbtor_other 0.088 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003 r_xyhbond_nbd_other r_metal_ion_other 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 3342 Nucleic Acid Atoms Solvent Atoms 553 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing