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Human MMP12 catalytic domain in complex with*N*-Hydroxy-2-(2-(4-methoxyphenyl)ethylsulfonamido)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 0.1M TRIS-HCL, 30% PEG 6000, 1M LICL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.989 α = 90 b = 61.107 β = 114.5 c = 54.213 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 2006-03-12 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 2 30.56 98.2 0.146 0.146 5 4.9 10122 10122 11.53
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 2 2.1 87.9 0.383 0.383 2.3 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 (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 2 30.56 9209 9209 913 98.16 0.23324 0.23324 0.2271 0.2268 0.29268 0.2909 RANDOM 13.6
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] -0.23 -0.77 -0.42 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.296 r_dihedral_angle_4_deg 16.86 r_dihedral_angle_3_deg 15.034 r_dihedral_angle_1_deg 7.094 r_scangle_it 3.976 r_scbond_it 3 r_mcangle_it 2.045 r_angle_refined_deg 1.696 r_mcbond_it 1.358 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.296 r_dihedral_angle_4_deg 16.86 r_dihedral_angle_3_deg 15.034 r_dihedral_angle_1_deg 7.094 r_scangle_it 3.976 r_scbond_it 3 r_mcangle_it 2.045 r_angle_refined_deg 1.696 r_mcbond_it 1.358 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.226 r_symmetry_hbond_refined 0.186 r_metal_ion_refined 0.165 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 24
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling