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Crystal structure of MMP12 in complex with hydroxamate inhibitor LP168.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Drops: 1 micro-L hMMP12 at 927 micro-M + 10 mM acetohydroxamic acid, LP168 at 1 milli-M and 1 micro-L precipitant.
Precipitant: 17% PEG 20K, 0.2 M imidazole malate, pH 8.5, 0.250 M NaCl
cryoprotectant: 27% PEG8K, 15% MPEG550, 10% glycerol, 90mM Tris-HCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2 38.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.41 α = 90 b = 67.09 β = 90 c = 68.44 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 100 CCD ADSC QUANTUM 315r mirrors 2010-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9184 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.59 47.91 99.7 0.123 12.1 7.93 38794 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.68 100 0.85 2.9 8.11
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 4H76 1.59 47.91 36745 1934 99.9 0.175 0.174 0.1832 0.202 0.2041 RANDOM 18.65
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] -1.15 1.77 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.77 r_dihedral_angle_4_deg 14.554 r_dihedral_angle_3_deg 11.556 r_dihedral_angle_1_deg 6.695 r_long_range_B_refined 6.469 r_long_range_B_other 6.11 r_scangle_other 4.581 r_scbond_it 3.061 r_scbond_other 3.061 r_mcangle_other 2.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.77 r_dihedral_angle_4_deg 14.554 r_dihedral_angle_3_deg 11.556 r_dihedral_angle_1_deg 6.695 r_long_range_B_refined 6.469 r_long_range_B_other 6.11 r_scangle_other 4.581 r_scbond_it 3.061 r_scbond_other 3.061 r_mcangle_other 2.878 r_mcangle_it 2.874 r_mcbond_it 2.021 r_mcbond_other 1.989 r_angle_refined_deg 1.767 r_angle_other_deg 1.093 r_chiral_restr 0.133 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_bond_other_d 0.006 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 2372 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing