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Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 1.7000M (NH4)2SO4, 15.0000% Glycerol, 1.7000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.85 α = 90 b = 46.85 β = 90 c = 94.94 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 300 mm CCD Adjustable focusing mirrors in K-B geometry 2008-10-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.94645,0.97965 APS 23-ID-B
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 1.8 24.953 96.6 0.065 7.1 2.86 21525 -3 19.864
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 1.8 1.86 92.7 0.491 1.44
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 1.8 24.953 21489 1044 99.74 0.154 0.152 0.1629 0.196 0.2019 RANDOM 31.881
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] 0.41 0.21 0.41 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.571 r_dihedral_angle_3_deg 11.939 r_dihedral_angle_4_deg 8.859 r_dihedral_angle_1_deg 6.733 r_scangle_it 3.213 r_scbond_it 1.995 r_angle_refined_deg 1.509 r_mcangle_it 1.214 r_angle_other_deg 0.774 r_mcbond_it 0.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.571 r_dihedral_angle_3_deg 11.939 r_dihedral_angle_4_deg 8.859 r_dihedral_angle_1_deg 6.733 r_scangle_it 3.213 r_scbond_it 1.995 r_angle_refined_deg 1.509 r_mcangle_it 1.214 r_angle_other_deg 0.774 r_mcbond_it 0.756 r_symmetry_vdw_other 0.234 r_mcbond_other 0.214 r_nbd_refined 0.199 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.138 r_symmetry_vdw_refined 0.127 r_chiral_restr 0.093 r_nbtor_other 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1776 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 27
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