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Crystal structure of M61 peptidase (bestatin-bound) from Xanthomonas campestris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 8J9C partially refined
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.5 294 0.1M Tris-Cl pH 8.5, 0.1M NaCl, 6-11% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.43 49.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.008 α = 90 b = 95.196 β = 104.472 c = 144.489 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 225 mm CCD Mirrors 2017-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.979490 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 1.9 47.6 99.4 0.066 0.08 0.045 0.997 13.4 2.9 215479 20.57
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 1.9 1.93 92.4 0.395 0.495 0.293 0.828 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 44.36 1.34 215351 10802 99.37 0.1722 0.1712 0.1718 0.1909 0.192 22.56
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 13.2952 f_angle_d 0.7266 f_chiral_restr 0.0485 f_plane_restr 0.0052 f_bond_d 0.0041
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19064 Nucleic Acid Atoms Solvent Atoms 2182 Heterogen Atoms 114
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing RESOLVE model building Coot model building PHENIX refinement