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Crystal structure of a Putative Metal-dependent Hydrolase (YP_001336084.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.20 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 1.0000M (NH4)2HPO4, 0.2000M NaCl, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 52.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.05 α = 90 b = 131.05 β = 90 c = 37.15 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 mirror (vertical focusing) 2008-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 2.2 29.311 99.9 0.081 0.081 5.9 7.1 17061
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 2.2 2.26 100 0.678 0.678 1.1 7.3 1212
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 2.2 29.311 16997 861 99.74 0.172 0.171 0.1742 0.202 0.2075 RANDOM 37.533
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] 1.14 1.14 -2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.303 r_dihedral_angle_4_deg 16.88 r_dihedral_angle_3_deg 13.22 r_scangle_it 7.315 r_scbond_it 5.566 r_dihedral_angle_1_deg 4.983 r_mcangle_it 3.215 r_mcbond_it 2.144 r_angle_refined_deg 1.375 r_angle_other_deg 0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.303 r_dihedral_angle_4_deg 16.88 r_dihedral_angle_3_deg 13.22 r_scangle_it 7.315 r_scbond_it 5.566 r_dihedral_angle_1_deg 4.983 r_mcangle_it 3.215 r_mcbond_it 2.144 r_angle_refined_deg 1.375 r_angle_other_deg 0.928 r_mcbond_other 0.464 r_symmetry_vdw_other 0.335 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.185 r_nbd_other 0.183 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.089 r_nbtor_other 0.087 r_symmetry_hbond_refined 0.079 r_bond_refined_d 0.016 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 1664 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHARP phasing