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Crystal structure of human MMP-2 catalytic domain in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 16 % w/v Polyethylene glycol 8,000, 20 % v/v Glycerol, 40 mM Potassium di-hydrogen phosphate
Crystal Properties Matthews coefficient Solvent content 2.69 54.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.683 α = 90 b = 79.683 β = 90 c = 127.434 γ = 90
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 PILATUS 200K 2019-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54184
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 2.4 21.78 99.8 0.976 5.7 11.5 15535
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.567 1.3 11.7
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 3AYU 2.4 21.78 14715 799 99.73 0.26794 0.26515 0.27 0.31892 0.3221 RANDOM 34.291
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] 0.3 0.3 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.474 r_dihedral_angle_3_deg 18.96 r_dihedral_angle_4_deg 17.575 r_long_range_B_refined 9.506 r_long_range_B_other 9.505 r_dihedral_angle_1_deg 7.481 r_mcangle_other 4.93 r_mcangle_it 4.923 r_scangle_other 4.267 r_mcbond_it 3.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.474 r_dihedral_angle_3_deg 18.96 r_dihedral_angle_4_deg 17.575 r_long_range_B_refined 9.506 r_long_range_B_other 9.505 r_dihedral_angle_1_deg 7.481 r_mcangle_other 4.93 r_mcangle_it 4.923 r_scangle_other 4.267 r_mcbond_it 3.033 r_mcbond_other 3.017 r_scbond_it 2.648 r_scbond_other 2.647 r_angle_refined_deg 1.601 r_angle_other_deg 1.22 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 2630 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing