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X-ray structure of MMP-13 in Complex with 4-(1,2,3-thiadiazol-4-yl)pyridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XUD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10% w/v PEG4000, 1 M ammonium formate, and 100 mM Tris, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.31 46.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.764 α = 90 b = 35.987 β = 130.55 c = 95.724 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 PIXEL DECTRIS PILATUS3 S 6M 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9840 SLS X06SA
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 72.74 98.8 0.169 2.6 3.3 24211
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 2.08 99.4 0.1978 3.3
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 1XUD 2 72.74 22822 1202 99.23 0.2012 0.1978 0.2077 0.2642 0.2629 RANDOM 21.911
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] -0.5 -0.31 0.15 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.898 r_dihedral_angle_4_deg 16.999 r_dihedral_angle_3_deg 12.862 r_dihedral_angle_1_deg 5.914 r_angle_refined_deg 1.075 r_angle_other_deg 0.785 r_symmetry_vdw_other 0.193 r_nbd_refined 0.188 r_nbtor_refined 0.185 r_nbd_other 0.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.898 r_dihedral_angle_4_deg 16.999 r_dihedral_angle_3_deg 12.862 r_dihedral_angle_1_deg 5.914 r_angle_refined_deg 1.075 r_angle_other_deg 0.785 r_symmetry_vdw_other 0.193 r_nbd_refined 0.188 r_nbtor_refined 0.185 r_nbd_other 0.171 r_symmetry_hbond_refined 0.153 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.147 r_metal_ion_refined 0.125 r_nbtor_other 0.083 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2651 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling CCP4 phasing