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Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor NNGH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OS9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Tris, PEG6000, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.19 α = 90 b = 62.56 β = 90 c = 37.26 γ = 90
Symmetry Space Group P 21 21 2
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 MARRESEARCH 2003-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.2000 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.34 46.407 98.4 7.2 6.2 36295
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.41 92.6 0.308 2.3 4.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1OS9 1.34 20 33671 2575 98.5 0.15789 0.15515 0.1945 0.2154 RANDOM 21.754
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] -1.5 -0.52 2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.048 r_sphericity_free 26.636 r_dihedral_angle_3_deg 13.286 r_sphericity_bonded 8.864 r_dihedral_angle_4_deg 8.52 r_dihedral_angle_1_deg 6.396 r_long_range_B_refined 3.85 r_rigid_bond_restr 3.31 r_long_range_B_other 3.207 r_scangle_other 2.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.048 r_sphericity_free 26.636 r_dihedral_angle_3_deg 13.286 r_sphericity_bonded 8.864 r_dihedral_angle_4_deg 8.52 r_dihedral_angle_1_deg 6.396 r_long_range_B_refined 3.85 r_rigid_bond_restr 3.31 r_long_range_B_other 3.207 r_scangle_other 2.303 r_mcangle_it 2.025 r_mcangle_other 2.024 r_scbond_it 2.021 r_scbond_other 2.02 r_angle_refined_deg 1.803 r_mcbond_it 1.758 r_mcbond_other 1.721 r_angle_other_deg 1.229 r_chiral_restr 0.35 r_bond_refined_d 0.035 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 1246 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing