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Tissue Inhibitor of Matrix Metalloproteinase-1 (TIMP-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293.15 0.2 M Lithium Citrate tribasic tetrahydrate,
20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.165 α = 90 b = 61.324 β = 90 c = 87.737 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS EIGER X 4M 2024-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2 43.87 97.7 0.074 0.1 0.067 0.992 8.7 3 12629
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.05 99.8 0.296 0.398 0.265 0.912 1.1 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 43.868 12603 569 96.671 0.202 0.1995 0.1996 0.255 0.2548 RANDOM 40.619
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] -1.323 5.109 -3.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.172 r_dihedral_angle_6_deg 15.315 r_dihedral_angle_2_deg 14.969 r_lrange_it 11.014 r_lrange_other 11.014 r_dihedral_angle_1_deg 9.02 r_scangle_other 8.41 r_scangle_it 8.409 r_mcangle_it 7.797 r_mcangle_other 7.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.172 r_dihedral_angle_6_deg 15.315 r_dihedral_angle_2_deg 14.969 r_lrange_it 11.014 r_lrange_other 11.014 r_dihedral_angle_1_deg 9.02 r_scangle_other 8.41 r_scangle_it 8.409 r_mcangle_it 7.797 r_mcangle_other 7.794 r_scbond_it 6.061 r_scbond_other 6.049 r_mcbond_it 5.301 r_mcbond_other 5.289 r_angle_refined_deg 2.254 r_angle_other_deg 0.922 r_symmetry_xyhbond_nbd_refined 0.197 r_nbd_refined 0.19 r_nbtor_refined 0.178 r_symmetry_nbd_other 0.175 r_nbd_other 0.156 r_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.131 r_chiral_restr 0.121 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1319 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling DIALS data reduction gemmi data extraction REFMAC refinement Aimless data scaling DIALS data reduction gemmi data extraction REFMAC refinement DIMPLE phasing