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Crystal structure of putative nucleic acid-binding lipoprotein (YP_001337197.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.46 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 31.0% polyethylene glycol 600, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.19 61.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.42 α = 90 b = 105.507 β = 90 c = 181.25 γ = 90
Symmetry Space Group P 21 21 21
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 2008-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.46 29.881 99.8 0.111 0.111 4.443 7.5 68362 50.365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.52 99.7 0.696 0.696 1.1 7.6 4955
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 SAD THROUGHOUT 2.46 29.881 68310 3458 99.71 0.194 0.192 0.1875 0.228 0.2203 RANDOM 35.156
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] -0.67 0.2 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.724 r_dihedral_angle_4_deg 19.472 r_dihedral_angle_3_deg 13.443 r_dihedral_angle_1_deg 3.554 r_mcangle_it 1.718 r_angle_refined_deg 1.698 r_scangle_it 1.515 r_mcbond_it 1.159 r_scbond_it 1.088 r_angle_other_deg 0.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.724 r_dihedral_angle_4_deg 19.472 r_dihedral_angle_3_deg 13.443 r_dihedral_angle_1_deg 3.554 r_mcangle_it 1.718 r_angle_refined_deg 1.698 r_scangle_it 1.515 r_mcbond_it 1.159 r_scbond_it 1.088 r_angle_other_deg 0.932 r_symmetry_vdw_other 0.286 r_mcbond_other 0.276 r_nbd_refined 0.209 r_nbd_other 0.191 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.146 r_symmetry_vdw_refined 0.146 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.098 r_nbtor_other 0.09 r_bond_refined_d 0.017 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 9080 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing