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Crystal structure of MMP12 in complex with carboxylic inhibitor LP165.
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 Drop: 1 micro-L (hMMP-12 at 855 micro-M + 1 milli-M hydroxamic acid + 1 milli-M LP165) and 1 micro-L reservoir solution.
Precipitant: 17% PEG 20K, 0.2M imidazole malate
250mM NaCl, pH 8.5.
Cryoprotection: 40% MPEG 5K, 10% 1,2-propanediol, 10% AAB (sodium acetate, ADA, bicine: 90% basic/10% acid), pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.16 α = 90 b = 59.86 β = 115.73 c = 53.94 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 ADSC QUANTUM 315r 2nd mirror Zerodur with Pt coating 2010-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979696 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.3 49 79.7 0.999 14.42 4.14 28894 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.38 31.8 1.31 0.343 1.02 3.68
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 1.3 48.59 26772 1996 79.7 0.145 0.142 0.1509 0.179 0.1856 RANDOM 18.43
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] 0.4 -0.06 -0.39 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.86 r_sphericity_free 21.923 r_dihedral_angle_4_deg 18.752 r_dihedral_angle_3_deg 13.302 r_sphericity_bonded 7.583 r_rigid_bond_restr 6.98 r_dihedral_angle_1_deg 5.775 r_long_range_B_refined 3.854 r_long_range_B_other 3.597 r_scangle_other 3.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.86 r_sphericity_free 21.923 r_dihedral_angle_4_deg 18.752 r_dihedral_angle_3_deg 13.302 r_sphericity_bonded 7.583 r_rigid_bond_restr 6.98 r_dihedral_angle_1_deg 5.775 r_long_range_B_refined 3.854 r_long_range_B_other 3.597 r_scangle_other 3.312 r_scbond_it 2.9 r_scbond_other 2.899 r_mcangle_it 2.481 r_mcangle_other 2.481 r_mcbond_it 2.147 r_mcbond_other 2.135 r_angle_other_deg 1.936 r_angle_refined_deg 1.649 r_chiral_restr 0.113 r_bond_refined_d 0.072 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building