☰ Navigation Tabs
Crystal structure of MMP12 in complex with inhibitor BE7.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I03
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10 293 Protein: 1 micro-L MMP12 at 290 micro-M with 10 milli-M acetohydroxamate + 0.1 Micro-L BE6 from 10 milii-M in 100% DMSO
Precipitant: 17% PEG 20K, 250 milli-M NaCl, 100 milii-M TRIS HCl, pH 10.0.
cryoprotectant: 40% (25 % di-ethylene glycol + 25 % glycerol + 25 % 1,2-propanediol) 10 % PEG 10K, 200 milli-M NaCl, 100 milli-M AAB (Na acetate,N-(2-Acetamido)iminodiacetic acid (ADA), Bicine) 10% acid/90% basic
Crystal Properties Matthews coefficient Solvent content 2.16 43.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.56 α = 90 b = 60.35 β = 116.1 c = 54.56 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 PIXEL DECTRIS EIGER X 9M microfocus 2016-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980035 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 1.2 36.74 99.3 0.088 0.096 0.998 10.21 6.61 46976 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.23 94.7 1.65 1.8 0.32 0.98 6.18
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 4I03 1.2 36.74 44626 2349 99.43 0.14574 0.1442 0.17523 0.1898 RANDOM 20.711
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] 0.22 -0.21 -0.05 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.284 r_sphericity_free 22.953 r_dihedral_angle_4_deg 18.293 r_dihedral_angle_3_deg 14.134 r_sphericity_bonded 10.025 r_rigid_bond_restr 8.512 r_dihedral_angle_1_deg 6.259 r_long_range_B_refined 5.075 r_long_range_B_other 4.875 r_scbond_it 4.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.284 r_sphericity_free 22.953 r_dihedral_angle_4_deg 18.293 r_dihedral_angle_3_deg 14.134 r_sphericity_bonded 10.025 r_rigid_bond_restr 8.512 r_dihedral_angle_1_deg 6.259 r_long_range_B_refined 5.075 r_long_range_B_other 4.875 r_scbond_it 4.594 r_scbond_other 4.594 r_scangle_other 4.587 r_mcangle_it 3.878 r_mcangle_other 3.877 r_mcbond_it 2.95 r_mcbond_other 2.948 r_angle_refined_deg 2.377 r_angle_other_deg 1.18 r_chiral_restr 0.154 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 1246 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building