☰ Navigation Tabs
Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor NNGH at 1.3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OS9 pdb entry 1OS9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Tris, PEG6000, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.194 α = 90 b = 62.564 β = 90 c = 37.262 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 MARRESEARCH double-crystal monochromator Si(111) and Si(220) 2003-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.20000 ELETTRA 5.2R
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 1.34 46.407 98.4 0.057 0.057 7.2 6.2 36295 36295 16.389
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) 1.34 1.41 92.6 0.308 0.308 2.3 4.8 4889
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb entry 1OS9 1.34 20 33678 33678 2578 100 0.18111 0.18111 0.17857 0.1857 0.2149 0.2157 RANDOM 18.214
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] -1.38 -0.72 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.416 r_sphericity_free 3.899 r_scangle_it 3.53 r_sphericity_bonded 3.012 r_scbond_it 2.461 r_mcangle_it 2.067 r_angle_refined_deg 1.668 r_mcbond_it 1.373 r_rigid_bond_restr 1.352 r_angle_other_deg 1.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.416 r_sphericity_free 3.899 r_scangle_it 3.53 r_sphericity_bonded 3.012 r_scbond_it 2.461 r_mcangle_it 2.067 r_angle_refined_deg 1.668 r_mcbond_it 1.373 r_rigid_bond_restr 1.352 r_angle_other_deg 1.006 r_symmetry_vdw_other 0.284 r_nbd_other 0.246 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.217 r_chiral_restr 0.197 r_xyhbond_nbd_refined 0.181 r_metal_ion_refined 0.107 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.009 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1246 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing