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Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor (R)-2-(biphenyl-4-ylsulfonamido)-4-methylpentanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y93 PDB ENTRY 1Y93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M Tris, 30% PEG 8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.181 α = 90 b = 60.554 β = 115.9 c = 54.428 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 Mirrors 2008-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54056
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 1.9 30.275 98 0.064 0.064 11.2 6.5 11585 11585 8.7
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) 1.9 2 91.3 0.169 0.169 9.1 3.4 1553
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1Y93 1.9 30.275 10560 10560 1024 100 0.16624 0.16624 0.16287 0.1638 0.20083 0.1994 RANDOM 9.04
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] 0.17 -0.14 -0.11 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.059 r_dihedral_angle_4_deg 14.634 r_dihedral_angle_3_deg 13.164 r_sphericity_free 6.964 r_dihedral_angle_1_deg 5.968 r_scangle_it 3.933 r_scbond_it 2.528 r_angle_refined_deg 1.613 r_mcangle_it 1.568 r_mcbond_it 0.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.059 r_dihedral_angle_4_deg 14.634 r_dihedral_angle_3_deg 13.164 r_sphericity_free 6.964 r_dihedral_angle_1_deg 5.968 r_scangle_it 3.933 r_scbond_it 2.528 r_angle_refined_deg 1.613 r_mcangle_it 1.568 r_mcbond_it 0.926 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 29
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling