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Human collagenase 3 (MMP-13) full form with peptides from pro-domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SLOW COOLING 7.5 277 propeptide impurity induces crystallization on cold storage Cryoprotectant: 10% PEG 10K, 5% di-ethylene glycol, 20% 1.2-propanediol, 5% glycerol, .2 M NaCl, 10% PCTP buffer 8:2 ratio, pH 7.5, SLOW COOLING, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.92 57.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.26 α = 90 b = 105.9 β = 102.11 c = 101.18 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 IMAGE PLATE MAR scanner 345 mm plate Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry 2011-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.872600 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.54 50 99.7 0.258 0.224 8.47 4.05 69045 68894 -3 39.978
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 2.54 2.69 99.4 1.114 0.965 1.63 4.01 11079
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 4FVL 2.54 49.503 -3 1.99 68882 68865 3442 99.8 0.1724 0.1689 0.1746 0.2413 0.2428 RANDOM 28.877
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 15.878 f_angle_d 1.189 f_chiral_restr 0.082 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12779 Nucleic Acid Atoms Solvent Atoms 896 Heterogen Atoms 287
Software Software Software Name Purpose DNA data collection MOLREP phasing PHENIX refinement XDS data reduction XDS data scaling