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Human MMP-12 complexed with the peptide IAG
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, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.888 α = 90 b = 60.358 β = 115.73 c = 54.521 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 ADSC QUANTUM 315 Double crystal, Si(111) or Si(311) 2006-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.15 49.08 94.6 0.059 0.059 4.2 6.8 50850 50850 11.08
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) 1.15 1.21 91.1 0.156 0.156 4.1 6.8 7153
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 1.15 36.96 46196 46196 4653 100 0.19942 0.19942 0.19713 0.1983 0.2225 0.2257 RANDOM 14.16
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] -0.07 -0.08 0.11 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.255 r_dihedral_angle_4_deg 10.841 r_dihedral_angle_3_deg 10.507 r_dihedral_angle_1_deg 5.769 r_sphericity_free 3.282 r_scangle_it 2.304 r_sphericity_bonded 2.019 r_rigid_bond_restr 1.756 r_scbond_it 1.655 r_mcangle_it 1.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.255 r_dihedral_angle_4_deg 10.841 r_dihedral_angle_3_deg 10.507 r_dihedral_angle_1_deg 5.769 r_sphericity_free 3.282 r_scangle_it 2.304 r_sphericity_bonded 2.019 r_rigid_bond_restr 1.756 r_scbond_it 1.655 r_mcangle_it 1.315 r_angle_refined_deg 1.093 r_angle_other_deg 0.978 r_mcbond_it 0.897 r_mcbond_other 0.357 r_nbd_refined 0.223 r_symmetry_vdw_other 0.2 r_symmetry_vdw_refined 0.195 r_nbd_other 0.186 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.097 r_nbtor_other 0.084 r_metal_ion_refined 0.084 r_chiral_restr 0.067 r_bond_other_d 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1255 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing