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The structure of the catalytic module of the metalloprotease ZmpA from Clostridium perfringens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.1 M MES:NaOH and 12% PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.168 α = 90 b = 54.553 β = 93.2 c = 90.984 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 ADSC QUANTUM 315r 2016-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97530 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.1 35 100 0.212 0.084 0.963 9.7 7.4 34596
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 0.96 0.386 0.734 2.3 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 5KDN 2.1 30.78 32145 1746 97.18 0.191 0.189 0.189 0.2277 0.2279 RANDOM 26.031
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] -0.03 0.2 -0.11 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.686 r_dihedral_angle_4_deg 14.641 r_dihedral_angle_3_deg 13.629 r_dihedral_angle_1_deg 6.745 r_angle_refined_deg 1.105 r_chiral_restr 0.094 r_gen_planes_refined 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3973 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 44
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction