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Crystal structure of a Putative Metal-dependent Hydrolase (YP_001336084.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.95 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 10.0000% polyethylene glycol 6000, 1.0000M lithium chloride, 0.1M Bicine pH 9.0, 0.001 M zinc chloride, 0.001 M Leucine-Chloromethyl ketone, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.19 α = 90 b = 131.19 β = 90 c = 37.12 γ = 90
Symmetry Space Group P 41 21 2
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 2009-01-17 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) 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 1.95 46.374 99.8 0.071 14.52 24283 -3 36.556
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 1.95 2.04 99.8 0.977 2.1
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 SAD THROUGHOUT 1.95 46.374 24240 1244 99.87 0.184 0.183 0.213 0.2499 RANDOM 30.899
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 0.15 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.65 r_dihedral_angle_4_deg 21.485 r_dihedral_angle_3_deg 12.096 r_scangle_it 6.735 r_dihedral_angle_1_deg 5.153 r_scbond_it 4.836 r_mcangle_it 2.93 r_mcbond_it 1.728 r_angle_refined_deg 1.276 r_angle_other_deg 0.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.65 r_dihedral_angle_4_deg 21.485 r_dihedral_angle_3_deg 12.096 r_scangle_it 6.735 r_dihedral_angle_1_deg 5.153 r_scbond_it 4.836 r_mcangle_it 2.93 r_mcbond_it 1.728 r_angle_refined_deg 1.276 r_angle_other_deg 0.918 r_mcbond_other 0.39 r_chiral_restr 0.074 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1737 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 23
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