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Uninhibited form of human MMP-12
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 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.545 α = 90 b = 60.751 β = 115.64 c = 54.264 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 MARRESEARCH Fixed exit double crystal Si [111], horizontally focussing 2006-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
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 1.24 19.63 97.2 0.079 0.079 3.8 5.8 41969 41969 7.17
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) 1.24 1.3 84.8 0.126 0.126 5.1 5.2 5315
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 1.24 19.64 38164 38164 3804 100 0.1984 0.1984 0.1966 0.1961 0.2163 0.216 RANDOM 10.993
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 -0.18 0.09 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.493 r_dihedral_angle_4_deg 11.622 r_dihedral_angle_3_deg 11.215 r_dihedral_angle_1_deg 5.597 r_sphericity_free 2.602 r_scangle_it 2.141 r_sphericity_bonded 2.127 r_scbond_it 1.516 r_mcangle_it 1.149 r_angle_refined_deg 1.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.493 r_dihedral_angle_4_deg 11.622 r_dihedral_angle_3_deg 11.215 r_dihedral_angle_1_deg 5.597 r_sphericity_free 2.602 r_scangle_it 2.141 r_sphericity_bonded 2.127 r_scbond_it 1.516 r_mcangle_it 1.149 r_angle_refined_deg 1.031 r_rigid_bond_restr 0.85 r_mcbond_it 0.745 r_nbtor_refined 0.302 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.085 r_symmetry_hbond_refined 0.084 r_metal_ion_refined 0.08 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing