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Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CIZ PDB entry 1CIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 Protein concentration: 7-20 mg/ml. Well solution: 18-22% PEG MME 5000, 0.2M Lithium sulfate, 0.1M Hepes buffer. 2-4 microliter drops with 1:1 ratio of protein complex solution and well solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.764 α = 90 b = 36.343 β = 93.53 c = 71.684 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 MAR CCD 165 mm mirrors 2000-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.74 70.71 96.5 0.056 17.7 2.9 37780 2 16.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.78 67.5 0.226 1.9 2606
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 entry 1CIZ 1.74 70.71 3 37780 35279 1847 98.57 0.168 0.167 0.1653 0.191 0.1898 RANDOM 17.075
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] 0.43 0.18 -0.48 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.128 r_dihedral_angle_4_deg 16.726 r_dihedral_angle_3_deg 12.382 r_dihedral_angle_1_deg 5.43 r_scangle_it 1.66 r_scbond_it 1.132 r_angle_refined_deg 1.043 r_mcangle_it 0.788 r_mcbond_it 0.453 r_symmetry_metal_ion_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.128 r_dihedral_angle_4_deg 16.726 r_dihedral_angle_3_deg 12.382 r_dihedral_angle_1_deg 5.43 r_scangle_it 1.66 r_scbond_it 1.132 r_angle_refined_deg 1.043 r_mcangle_it 0.788 r_mcbond_it 0.453 r_symmetry_metal_ion_refined 0.326 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.181 r_symmetry_hbond_refined 0.116 r_metal_ion_refined 0.109 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2651 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 82
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction AMoRE phasing