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Human catalytic MMP-12 in complex with 5-(1,2-dithiolan-3-yl)-N-(3-hydroxypropyl)pentanamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1 M Tris-HCl, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.15 42.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.79 α = 90 b = 60.17 β = 114.61 c = 53.73 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 OXFORD ONYX CCD 2016-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54
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 1.8 25.63 94.5 0.062 24.1 6.8 12935 22.3
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 1.8 1.9 78.3 0.42 3.65 4.2
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 1Y93 1.8 25.62 12282 647 95.14 0.17017 0.16721 0.1805 0.22736 0.2081 RANDOM 16.315
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] 1.14 -0.11 -0.47 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.953 r_dihedral_angle_4_deg 14.032 r_dihedral_angle_3_deg 13.199 r_long_range_B_refined 7.686 r_long_range_B_other 7.467 r_dihedral_angle_1_deg 7.036 r_scangle_other 3.48 r_scbond_it 2.236 r_angle_refined_deg 2.16 r_scbond_other 2.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.953 r_dihedral_angle_4_deg 14.032 r_dihedral_angle_3_deg 13.199 r_long_range_B_refined 7.686 r_long_range_B_other 7.467 r_dihedral_angle_1_deg 7.036 r_scangle_other 3.48 r_scbond_it 2.236 r_angle_refined_deg 2.16 r_scbond_other 2.099 r_mcangle_other 1.885 r_mcangle_it 1.879 r_angle_other_deg 1.225 r_mcbond_it 1.153 r_mcbond_other 1.092 r_chiral_restr 0.138 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1227 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing