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Crystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 30.000000000% PEG-400, 0.200000000M LiSO4, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.336 α = 90 b = 61.572 β = 108.5 c = 52.804 γ = 90
Symmetry Space Group C 1 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 mirror (vertical focusing) 2010-06-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.95369,0.97951,0.97905 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 28.576 99.9 0.079 8.5 3.2 36639 36639 16.68
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 1.6 1.64 100 0.393 0.393 1.9 3.1 2681
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 1.6 28.576 36638 1825 99.82 0.1504 0.1491 0.1635 0.1751 0.1916 RANDOM 22.2315
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] 1.64 0.77 -0.3 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.963 r_dihedral_angle_4_deg 17.879 r_dihedral_angle_3_deg 12.347 r_dihedral_angle_1_deg 6.077 r_scangle_it 5.871 r_scbond_it 4.094 r_mcangle_it 2.954 r_mcbond_it 1.801 r_angle_refined_deg 1.587 r_angle_other_deg 1.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.963 r_dihedral_angle_4_deg 17.879 r_dihedral_angle_3_deg 12.347 r_dihedral_angle_1_deg 6.077 r_scangle_it 5.871 r_scbond_it 4.094 r_mcangle_it 2.954 r_mcbond_it 1.801 r_angle_refined_deg 1.587 r_angle_other_deg 1.022 r_mcbond_other 0.471 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1994 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 82
Software Software Software Name Purpose SHELX phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing