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Crystal structure of Putative DNA-binding protein (YP_299413.1) from Ralstonia eutrophA JMP134 at 1.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 277 0.2000M NaCl, 20.0000% PEG-1000, 0.1M Na,K-Phosphate pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.89 35.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.897 α = 90 b = 53.897 β = 90 c = 111.1 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 collimating mirror, toroid focusing mirror 2009-03-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97929,0.97918 SSRL BL9-2
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 1.3 26.948 91.6 0.028 13.78 2.71 29085 -3 11.177
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 1.3 1.35 64 0.258 2.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.3 26.948 29085 1490 98.58 0.121 0.119 0.1239 0.14 0.1437 RANDOM 15.307
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] 0.2 0.1 0.2 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.949 r_dihedral_angle_3_deg 12.956 r_dihedral_angle_4_deg 11.397 r_sphericity_free 9.758 r_dihedral_angle_1_deg 6.584 r_scangle_it 4.475 r_sphericity_bonded 3.917 r_scbond_it 3.431 r_mcangle_it 2.304 r_rigid_bond_restr 1.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.949 r_dihedral_angle_3_deg 12.956 r_dihedral_angle_4_deg 11.397 r_sphericity_free 9.758 r_dihedral_angle_1_deg 6.584 r_scangle_it 4.475 r_sphericity_bonded 3.917 r_scbond_it 3.431 r_mcangle_it 2.304 r_rigid_bond_restr 1.899 r_mcbond_it 1.833 r_angle_refined_deg 1.644 r_angle_other_deg 0.845 r_mcbond_other 0.719 r_symmetry_vdw_other 0.312 r_symmetry_hbond_refined 0.308 r_nbd_other 0.207 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.197 r_nbtor_refined 0.175 r_symmetry_vdw_refined 0.135 r_chiral_restr 0.103 r_nbtor_other 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1101 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms
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