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Crystal structure MMP-9 complexes with a constrained hydroxamate based inhibitor LT4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.25 293 40% MPEG 5K, pH 7.25, 18% MPEG 2K
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.68 α = 90 b = 97.79 β = 90 c = 43.49 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 CCD ADSC QUANTUM 315r 2013-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980100 SOLEIL PROXIMA 2
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 1.83 43.495 99.8 0.212 0.188 9.57 4.73 28651 28592 -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 1.83 1.95 99.4 0.848 2.25 4.21
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4H3X 1.83 40.91 27162 1430 99.79 0.17461 0.17253 0.21368 0.1916 RANDOM 18.239
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 0.26 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.395 r_dihedral_angle_4_deg 18.213 r_dihedral_angle_3_deg 14.655 r_dihedral_angle_1_deg 7.301 r_long_range_B_refined 6.919 r_mcangle_it 2.706 r_scbond_it 2.4 r_angle_refined_deg 1.892 r_mcbond_it 1.74 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.395 r_dihedral_angle_4_deg 18.213 r_dihedral_angle_3_deg 14.655 r_dihedral_angle_1_deg 7.301 r_long_range_B_refined 6.919 r_mcangle_it 2.706 r_scbond_it 2.4 r_angle_refined_deg 1.892 r_mcbond_it 1.74 r_chiral_restr 0.147 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2608 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing