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Human MMP12 in complex with 3-(5-(1,2-dithiolan-3-yl)pentanamido)propane-1-sulfonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1 M Tris-HCl, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.16 42.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.926 α = 90 b = 60.47 β = 114.55 c = 53.844 γ = 90
Symmetry Space Group C 1 2 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 OXFORD ONYX CCD 2015-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 24.49 93.4 0.076 0.031 5.6 6.2 12916 8.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 77.4 0.175 0.175 3.1 1.8
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 1Y93 1.8 24.29 12255 660 93.34 0.12909 0.12545 0.1379 0.19533 0.2022 RANDOM 15.609
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] -0.48 -0.02 0.04 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.341 r_sphericity_free 19.178 r_dihedral_angle_3_deg 11.105 r_sphericity_bonded 10.549 r_rigid_bond_restr 8.034 r_dihedral_angle_1_deg 6.584 r_dihedral_angle_4_deg 6.014 r_scangle_other 4.71 r_scbond_it 4.296 r_scbond_other 3.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.341 r_sphericity_free 19.178 r_dihedral_angle_3_deg 11.105 r_sphericity_bonded 10.549 r_rigid_bond_restr 8.034 r_dihedral_angle_1_deg 6.584 r_dihedral_angle_4_deg 6.014 r_scangle_other 4.71 r_scbond_it 4.296 r_scbond_other 3.994 r_long_range_B_refined 3.919 r_long_range_B_other 3.852 r_mcangle_other 2.48 r_mcangle_it 2.468 r_mcbond_it 2.303 r_mcbond_other 2.284 r_angle_refined_deg 1.979 r_angle_other_deg 1.148 r_chiral_restr 0.13 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing