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Crystal structure of Putative carboxypeptidase A (YP_562911.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.39 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 15.0000% Glycerol, 0.1700M NH4OAc, 25.5000% PEG-4000, 0.1M Citrate pH 5.6, ADDITIVE: CALCIUM CHLORIDE 0.006 M, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 52.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.417 α = 90 b = 81.417 β = 90 c = 479.685 γ = 120
Symmetry Space Group P 61 2 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) 2009-07-09 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) 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 2.39 49.147 99.7 0.206 13.16 38954 -3 40.987
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 2.39 2.48 98.9 0.013 2.5
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 2.39 49.147 38841 1947 99.86 0.182 0.18 0.1777 0.233 0.2217 RANDOM 26.223
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] 2.15 1.07 2.15 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.031 r_dihedral_angle_4_deg 17.026 r_dihedral_angle_3_deg 12.924 r_scangle_it 6.828 r_dihedral_angle_1_deg 5.281 r_scbond_it 5.263 r_mcangle_it 2.65 r_mcbond_it 1.558 r_angle_refined_deg 1.546 r_angle_other_deg 0.907
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.031 r_dihedral_angle_4_deg 17.026 r_dihedral_angle_3_deg 12.924 r_scangle_it 6.828 r_dihedral_angle_1_deg 5.281 r_scbond_it 5.263 r_mcangle_it 2.65 r_mcbond_it 1.558 r_angle_refined_deg 1.546 r_angle_other_deg 0.907 r_mcbond_other 0.516 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5891 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 24
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