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Crystal structure of full-length human MMP-12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y93 1Y93, 1SU3 experimental model PDB 1SU3 1Y93, 1SU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1M Tris-HCl, 30% PEG8000, 200mM acetohydroxamic acid, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.87 57.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.037 α = 90 b = 60.148 β = 90.74 c = 59.611 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 Enhance Ultra 2006-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OXFORD DIFFRACTION ENHANCE ULTRA 1.5418
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 3 30.7 97.8 0.15 0.15 4.9 4.8 9308 9308 36.17
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) 3 3.16 97.7 0.43 0.43 1.8 4.7 1371
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 1Y93, 1SU3 3 30.7 8464 8464 844 100 0.24339 0.24339 0.23577 0.2415 0.319 0.3226 RANDOM 5.979
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] 0.58 2.03 0.21 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.192 r_dihedral_angle_4_deg 28.87 r_dihedral_angle_3_deg 28.029 r_dihedral_angle_1_deg 11.669 r_scangle_it 4.365 r_angle_refined_deg 4.271 r_scbond_it 3.23 r_mcangle_it 2.031 r_mcbond_it 1.517 r_symmetry_hbond_refined 0.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.192 r_dihedral_angle_4_deg 28.87 r_dihedral_angle_3_deg 28.029 r_dihedral_angle_1_deg 11.669 r_scangle_it 4.365 r_angle_refined_deg 4.271 r_scbond_it 3.23 r_mcangle_it 2.031 r_mcbond_it 1.517 r_symmetry_hbond_refined 0.593 r_symmetry_vdw_refined 0.449 r_nbd_refined 0.392 r_xyhbond_nbd_refined 0.384 r_nbtor_refined 0.382 r_metal_ion_refined 0.345 r_chiral_restr 0.329 r_bond_refined_d 0.049 r_gen_planes_refined 0.021 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_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2990 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling MOLREP phasing