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Crystal structure of the catalytic domain of MMP-13 complexed with a potent pyrimidinetrione inhibitor
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, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.09 41.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.089 α = 90 b = 108.223 β = 90 c = 36.035 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.06 20 20325 15989
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 Entry 830C 2.3 19.9 12847 1080 94.38 0.21507 0.20849 0.2084 0.29459 0.2932 RANDOM 22.893
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] -0.24 1.07 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.6 r_dihedral_angle_3_deg 19.781 r_dihedral_angle_4_deg 14.044 r_dihedral_angle_1_deg 7.984 r_scangle_it 3.485 r_scbond_it 2.696 r_angle_refined_deg 2.064 r_mcangle_it 1.726 r_mcbond_it 1.042 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.6 r_dihedral_angle_3_deg 19.781 r_dihedral_angle_4_deg 14.044 r_dihedral_angle_1_deg 7.984 r_scangle_it 3.485 r_scbond_it 2.696 r_angle_refined_deg 2.064 r_mcangle_it 1.726 r_mcbond_it 1.042 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.317 r_nbd_refined 0.233 r_symmetry_hbond_refined 0.219 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.157 r_metal_ion_refined 0.14 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 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 2637 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement