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Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 830C PDB ENTRY 830C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM MES, 200 mM magnesium acetate, 20 % PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.55 65.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.526 α = 90 b = 72.526 β = 90 c = 181.375 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Mirrors 1999-01-29 M SINGLE WAVELENGTH 2 1 100 IMAGE PLATE MAR scanner 345 mm plate Mirrors 1999-04-26
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418 2 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.0503 MPG/DESY, HAMBURG BW6
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 23.77 0.999 0.06 0.06 25.1 8.6 36318 36318 30.492
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) 2 2.07 0.999 0.498 0.498 0.031 4.5 3606
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 830C 2 23.77 34445 34445 1800 100 0.20144 0.20144 0.19991 0.2313 RANDOM 30.492
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] 1.48 0.74 1.48 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.653 r_dihedral_angle_1_deg 4.698 r_scangle_it 3.484 r_scbond_it 2.187 r_mcangle_it 1.653 r_angle_refined_deg 1.626 r_mcbond_it 0.898 r_angle_other_deg 0.795 r_symmetry_vdw_other 0.428 r_symmetry_vdw_refined 0.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.653 r_dihedral_angle_1_deg 4.698 r_scangle_it 3.484 r_scbond_it 2.187 r_mcangle_it 1.653 r_angle_refined_deg 1.626 r_mcbond_it 0.898 r_angle_other_deg 0.795 r_symmetry_vdw_other 0.428 r_symmetry_vdw_refined 0.392 r_metal_ion_refined 0.376 r_nbd_refined 0.278 r_xyhbond_nbd_refined 0.256 r_nbd_other 0.222 r_xyhbond_nbd_other 0.177 r_symmetry_hbond_refined 0.171 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_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 2725 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 4
Software Software Software Name Purpose DNA data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling