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Crystal structure of Putative metal-dependent hydrolase (YP_001302908.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 38.0000% polyethylene glycol 300, 0.2500M calcium acetate, 0.1M sodium cacodylate pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.034 α = 90 b = 95.034 β = 90 c = 63.295 γ = 120
Symmetry Space Group P 32 2 1
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 2009-05-15 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 2.3 29.54 99.6 0.22 0.22 10.2 7.4 14896 32.531
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 2.3 2.36 99 0.013 1.252 1.8 7.4 1103
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 2.3 29.54 14894 750 99.41 0.166 0.164 0.1784 0.204 0.2246 RANDOM 17.881
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] 1.9 0.95 1.9 -2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.986 r_dihedral_angle_3_deg 12.92 r_dihedral_angle_4_deg 12.167 r_dihedral_angle_1_deg 6.042 r_scangle_it 1.963 r_scbond_it 1.315 r_angle_refined_deg 1.059 r_mcangle_it 0.876 r_angle_other_deg 0.709 r_mcbond_it 0.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.986 r_dihedral_angle_3_deg 12.92 r_dihedral_angle_4_deg 12.167 r_dihedral_angle_1_deg 6.042 r_scangle_it 1.963 r_scbond_it 1.315 r_angle_refined_deg 1.059 r_mcangle_it 0.876 r_angle_other_deg 0.709 r_mcbond_it 0.461 r_chiral_restr 0.091 r_mcbond_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1734 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 36
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