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Crystal structure of human MMP-12 in complex with acetohydroxamic acid and a bicyclic inhibitor
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 8 298 0.1 M Tris-HCl, 30% PEG 6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.25 α = 90 b = 60.179 β = 114.59 c = 53.974 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 MAR CCD 165 mm Fixed exit double crystal Si [111], horizontally focusing 2005-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.93920 EMBL/DESY, HAMBURG BW7A
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 1.32 49.08 99.1 0.053 0.053 8.6 3.1 34648 34648 10.41
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) 1.32 1.39 95.6 0.282 0.282 2.1 2.9 4823
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 1.32 25.68 31503 31503 3144 100 0.16256 0.16256 0.16062 0.1584 0.18176 0.1817 RANDOM 13.577
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] 0.27 -0.33 -0.11 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.449 r_dihedral_angle_4_deg 16.79 r_dihedral_angle_3_deg 9.33 r_dihedral_angle_1_deg 5.72 r_sphericity_free 2.614 r_scangle_it 2.348 r_sphericity_bonded 1.86 r_scbond_it 1.837 r_rigid_bond_restr 1.751 r_mcangle_it 1.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.449 r_dihedral_angle_4_deg 16.79 r_dihedral_angle_3_deg 9.33 r_dihedral_angle_1_deg 5.72 r_sphericity_free 2.614 r_scangle_it 2.348 r_sphericity_bonded 1.86 r_scbond_it 1.837 r_rigid_bond_restr 1.751 r_mcangle_it 1.115 r_angle_refined_deg 1.1 r_mcbond_it 0.76 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.121 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.077 r_metal_ion_refined 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing