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Crystal structure of an MMP twin carboxylate based inhibitor LC20 in complex with the MMP-9 catalytic domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H82
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 Protein: human MMP9 (E402Q) at 308.7 micro-M twin inhibitor LC20 at 154 micro-M (stoichiometry 2:1) and 120mM acetohydroxamic acid.
RESERVOIR: 12% Polyethylene glycol 20,000, 1.5M NaCl, 0.1 M PCTP (Na propionate, Na cacodylate, Bis-Tris-propane ratio 2:1:2; 75% pH 4, 25% pH 9.5)
CRYOPROTECTANT: 40% C2 (25 % di-ethylene glycol + 25 % glycerol + 25 % 1,2-propanediol), 9% PEG 10,000 1.5M NaCl, 0.1M PCTP 80/2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.87 α = 90 b = 98.24 β = 90 c = 47.44 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 100 PIXEL PSI PILATUS 6M bent cylindrical mirror 2012-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98011 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.94 50 99.4 0.166 0.155 8.19 7.98 26173 26019 -3 36.556
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.06 96.6 1.533 1.432 1.3 7.87 4162
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 4H82 1.94 42.72 -3 26019 24713 1301 100 0.21439 0.21088 0.2141 0.28302 0.2845 RANDOM 32.048
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] 0.82 -0.65 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.336 r_dihedral_angle_4_deg 24.017 r_dihedral_angle_3_deg 16.531 r_dihedral_angle_1_deg 6.74 r_scangle_it 4.572 r_scbond_it 3.114 r_mcangle_it 2.12 r_angle_refined_deg 1.966 r_mcbond_it 1.241 r_chiral_restr 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.336 r_dihedral_angle_4_deg 24.017 r_dihedral_angle_3_deg 16.531 r_dihedral_angle_1_deg 6.74 r_scangle_it 4.572 r_scbond_it 3.114 r_mcangle_it 2.12 r_angle_refined_deg 1.966 r_mcbond_it 1.241 r_chiral_restr 0.158 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2550 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 190
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling