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Crystal structure of putative M16-like peptidase from Alicyclobacillus acidocaldarius
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.17 M Na acetate, 0.085 M Tris/HCl, pH 8.5, 25.5% PEG4000, 15% glycerol,chymotrypsin treated
Crystal Properties Matthews coefficient Solvent content 2.9 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.201 α = 90 b = 127.201 β = 90 c = 65.991 γ = 90
Symmetry Space Group P 43 21 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 ADSC QUANTUM 315r mirrors 2013-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97915 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 30 99.9 0.111 0.117 0.035 23.447 11.5 40177 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 100 0.431 0.754 2.03 11.4 1973
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 1.95 29.29 39985 1075 99.57 0.1824 0.1815 0.1882 0.214 0.2212 RANDOM 47.605
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] -0.81 -0.81 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.004 r_dihedral_angle_4_deg 17.149 r_dihedral_angle_3_deg 14.621 r_dihedral_angle_1_deg 6.111 r_scangle_it 3.475 r_scbond_it 2.254 r_angle_refined_deg 1.366 r_mcangle_it 1.271 r_angle_other_deg 0.868 r_mcbond_it 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.004 r_dihedral_angle_4_deg 17.149 r_dihedral_angle_3_deg 14.621 r_dihedral_angle_1_deg 6.111 r_scangle_it 3.475 r_scbond_it 2.254 r_angle_refined_deg 1.366 r_mcangle_it 1.271 r_angle_other_deg 0.868 r_mcbond_it 0.71 r_mcbond_other 0.214 r_chiral_restr 0.092 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 3386 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 22
Software Software Software Name Purpose SBC-Collect data collection REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data scaling MLPHARE phasing HKL-3000 phasing ARP model building SHELX phasing DM phasing HKL-3000 data reduction WARP model building SHELX model building DM model building