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X-ray structure of the catalytic domain of MMP-8 with the inhibitor ML115
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DPE PDB entry 3DPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 10 % PEG 6000, 0.2M MES/NAOH, 1M NA PHOSPHATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.91 α = 90 b = 68.69 β = 90 c = 70.69 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray PIXEL PSI PILATUS 6M 2013-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 1.2 49.26 99.17 0.09 10.2 45495 45495 12.98
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 1.2 1.3 99.2 0.456 2.52 10641
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 (All) 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 3DPE 1.2 49.26 45495 5056 99.17 0.17197 0.17197 0.16952 0.1723 0.1937 0.1951 RANDOM 9.976
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] 0.25 0.23 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.967 r_sphericity_free 22.661 r_dihedral_angle_4_deg 18.927 r_dihedral_angle_3_deg 11.074 r_sphericity_bonded 8.611 r_dihedral_angle_1_deg 6.996 r_rigid_bond_restr 2.739 r_long_range_B_refined 1.976 r_long_range_B_other 1.733 r_angle_refined_deg 1.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.967 r_sphericity_free 22.661 r_dihedral_angle_4_deg 18.927 r_dihedral_angle_3_deg 11.074 r_sphericity_bonded 8.611 r_dihedral_angle_1_deg 6.996 r_rigid_bond_restr 2.739 r_long_range_B_refined 1.976 r_long_range_B_other 1.733 r_angle_refined_deg 1.522 r_scangle_other 1.209 r_scbond_it 0.959 r_scbond_other 0.959 r_angle_other_deg 0.881 r_mcangle_it 0.839 r_mcangle_other 0.838 r_mcbond_it 0.808 r_mcbond_other 0.801 r_chiral_restr 0.135 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1282 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement XDS data reduction SCALA data scaling