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Crystal structure of a Putative gamma-D-glutamyl-L-diamino acid endopeptidase (DVU_0896) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 1.0000M LiCl, 20.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.08 40.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.337 α = 90 b = 54.465 β = 94.06 c = 122.982 γ = 90
Symmetry Space Group P 1 21 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 2010-01-24 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97918 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 1.75 29.594 98.1 0.045 11.19 78779 -3 20.246
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 1.75 1.81 96 0.446 2
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 1.75 29.594 78760 3951 99.35 0.141 0.139 0.1493 0.173 0.1806 RANDOM 20.803
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] 0.62 -1.88 -0.29 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.058 r_dihedral_angle_4_deg 16.11 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 6.066 r_scangle_it 5.814 r_scbond_it 4.072 r_mcangle_it 2.581 r_mcbond_it 1.675 r_angle_refined_deg 1.499 r_angle_other_deg 0.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.058 r_dihedral_angle_4_deg 16.11 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 6.066 r_scangle_it 5.814 r_scbond_it 4.072 r_mcangle_it 2.581 r_mcbond_it 1.675 r_angle_refined_deg 1.499 r_angle_other_deg 0.908 r_mcbond_other 0.642 r_chiral_restr 0.088 r_bond_refined_d 0.015 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 6455 Nucleic Acid Atoms Solvent Atoms 941 Heterogen Atoms 107
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