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Crystal structure of M1 zinc metallopeptidase from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.5 294 0.1M Bis-Tris pH 5.5, 0.23M Ammonium formate, 27% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.97 33.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.371 α = 89.74 b = 57.583 β = 82.3 c = 69.579 γ = 67.53
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2017-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.979476 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.045 45.3 97.3 0.064 0.076 0.041 0.997 14.8 3.3 45670 13.249
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 88.3 0.381 0.467 0.267 0.843 2.9 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1H19 2.045 30.251 1.98 45644 2243 97.28 0.1772 0.175 0.175 0.2201 0.2193
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.739 f_angle_d 0.905 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6639 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement Coot model building PHENIX model building MR-Rosetta phasing PHASER phasing Aimless data scaling XDS data reduction MAR345dtb data collection