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Crystal structure of a lipoprotein YedD (KPN_02420) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.38 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 30.00% polyethylene glycol 3000, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.84 33.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.81 α = 90 b = 51.067 β = 90 c = 52.436 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 ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2012-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 1.38 39.81 99.8 0.045 15.44 7 22613 -3 16.745
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 1.38 1.43 99.6 0.841 1.5
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 1.38 39.81 22564 1152 99.89 0.1509 0.1494 0.1587 0.1795 0.1847 RANDOM 21.1093
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] 0.15 0.08 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.573 r_dihedral_angle_4_deg 16.273 r_dihedral_angle_3_deg 13.045 r_sphericity_free 7.608 r_scangle_it 6.592 r_dihedral_angle_1_deg 6.041 r_scbond_it 4.694 r_sphericity_bonded 4.468 r_mcangle_it 4.03 r_mcbond_it 2.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.573 r_dihedral_angle_4_deg 16.273 r_dihedral_angle_3_deg 13.045 r_sphericity_free 7.608 r_scangle_it 6.592 r_dihedral_angle_1_deg 6.041 r_scbond_it 4.694 r_sphericity_bonded 4.468 r_mcangle_it 4.03 r_mcbond_it 2.601 r_rigid_bond_restr 1.912 r_mcbond_other 1.851 r_angle_refined_deg 1.567 r_angle_other_deg 1.025 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 910 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing