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Human MMP-12 catalytic domain in complex with*N*-Hydroxy-2-(2-phenylethylsulfonamido)acetamide
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% PEG6000, 1M LiCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.643 α = 90 b = 60.475 β = 115.15 c = 54.162 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 graphite 2005-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.5406
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 1.8 49.4 99 0.056 0.056 12.2 6.2 12352 12352 7.7
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 1.8 1.9 92.2 0.154 0.154 5 1.9
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 (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 1.81 36.99 11250 11250 1102 100 0.17553 0.16976 0.169 0.23595 0.2358 RANDOM 7.914
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] 0.05 -0.12 0.09 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.838 r_dihedral_angle_3_deg 11.887 r_dihedral_angle_4_deg 9.04 r_sphericity_free 6.881 r_dihedral_angle_1_deg 5.788 r_scangle_it 3.135 r_scbond_it 2.02 r_angle_refined_deg 1.637 r_mcangle_it 1.23 r_mcbond_it 0.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.838 r_dihedral_angle_3_deg 11.887 r_dihedral_angle_4_deg 9.04 r_sphericity_free 6.881 r_dihedral_angle_1_deg 5.788 r_scangle_it 3.135 r_scbond_it 2.02 r_angle_refined_deg 1.637 r_mcangle_it 1.23 r_mcbond_it 0.773 r_nbtor_refined 0.308 r_chiral_restr 0.229 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.14 r_metal_ion_refined 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 22
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling