☰ Navigation Tabs
Crystal structure of Putative metallopeptidase (YP_676511.1) from MESORHIZOBIUM SP. BNC1 at 2.13 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.29 277 0.01 M cobalt chloride, 1.636 M ammonium sulfate, 0.1 M MES pH 6.29, Additive: 0.001 M MANGANESE CHLORIDE, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.22 α = 90 b = 82.22 β = 90 c = 310.73 γ = 120
Symmetry Space Group P 62 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) 2009-07-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97883,0.91837 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 2.13 46.829 100 0.165 12.48 36013 -3 29.758
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 2.13 2.21 100 0.011 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 MAD THROUGHOUT 2.13 46.829 36013 1798 99.98 0.186 0.184 0.19 0.228 0.2353 RANDOM 22.601
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] 0.72 0.36 0.72 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.235 r_dihedral_angle_4_deg 15.304 r_dihedral_angle_3_deg 13.512 r_dihedral_angle_1_deg 6.461 r_scangle_it 3.439 r_scbond_it 2.247 r_angle_refined_deg 1.499 r_mcangle_it 1.286 r_angle_other_deg 0.91 r_mcbond_it 0.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.235 r_dihedral_angle_4_deg 15.304 r_dihedral_angle_3_deg 13.512 r_dihedral_angle_1_deg 6.461 r_scangle_it 3.439 r_scbond_it 2.247 r_angle_refined_deg 1.499 r_mcangle_it 1.286 r_angle_other_deg 0.91 r_mcbond_it 0.711 r_mcbond_other 0.192 r_chiral_restr 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3786 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 88
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