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Crystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain of TIMP-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CGL PDB ENTRIES 1CGL AND 1UEA experimental model PDB 1UEA PDB ENTRIES 1CGL AND 1UEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 10% PEG 8000, 8% ETHYLENE GLYCOL, 0.1M HEPES (PH 7.5).
Crystal Properties Matthews coefficient Solvent content 2.3 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.098 α = 90 b = 67.85 β = 100.29 c = 86.241 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 CCD MIRRORS 2002-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.54 40 98.4 0.09 8.3 6.5 29526 59.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.63 99.4 0.45 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 ENTRIES 1CGL AND 1UEA 2.54 23 28349 997 98.3 0.249 0.248 0.2465 0.275 0.267 RANDOM 45.04
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] 2.67 0.42 -0.9 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.444 r_dihedral_angle_3_deg 15.635 r_dihedral_angle_4_deg 11.954 r_dihedral_angle_1_deg 4.481 r_angle_refined_deg 0.892 r_scangle_it 0.421 r_nbtor_refined 0.295 r_scbond_it 0.265 r_mcangle_it 0.24 r_nbd_refined 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.444 r_dihedral_angle_3_deg 15.635 r_dihedral_angle_4_deg 11.954 r_dihedral_angle_1_deg 4.481 r_angle_refined_deg 0.892 r_scangle_it 0.421 r_nbtor_refined 0.295 r_scbond_it 0.265 r_mcangle_it 0.24 r_nbd_refined 0.169 r_symmetry_hbond_refined 0.154 r_mcbond_it 0.133 r_symmetry_vdw_refined 0.109 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6491 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing