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Human MMP-12 catalytic domain in complex with*(R)-N*-Hydroxy-1-(phenethylsulfonyl)pyrrolidine-2-carboxamide
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, 1 M LiCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.487 α = 90 b = 60.431 β = 115.21 c = 54.207 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 2005-12-16 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 30.2 96.6 0.093 0.093 7 6.5 11689 11689 8.42
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 84.5 0.267 0.267 2.8 2.2
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 1.82 30.2 10648 10648 1030 100 0.24152 0.23429 0.2359 0.31676 0.316 RANDOM 6.716
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] 0.16 -0.2 -0.28 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.488 r_dihedral_angle_4_deg 20.999 r_dihedral_angle_3_deg 16.563 r_sphericity_free 9.278 r_dihedral_angle_1_deg 7.693 r_scangle_it 3.131 r_scbond_it 2.334 r_angle_refined_deg 1.976 r_mcangle_it 1.367 r_mcbond_it 0.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.488 r_dihedral_angle_4_deg 20.999 r_dihedral_angle_3_deg 16.563 r_sphericity_free 9.278 r_dihedral_angle_1_deg 7.693 r_scangle_it 3.131 r_scbond_it 2.334 r_angle_refined_deg 1.976 r_mcangle_it 1.367 r_mcbond_it 0.957 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.301 r_nbd_refined 0.246 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.198 r_metal_ion_refined 0.157 r_chiral_restr 0.125 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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 93 Heterogen Atoms 25
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling