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Tissue inhibitor of 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 5.6 293.15 0.2 Ammonium Sulphate,
0.1 M tri-sodium citrate,
25% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.39 48.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.979 α = 90 b = 45.542 β = 99.876 c = 90.347 γ = 90
Symmetry Space Group P 1 21 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 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 2.3 45.84 99.1 0.152 0.21 0.144 0.983 4.7 3.5 17537
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) 2.3 2.38 99.9 0.93 1.28 0.876 0.664 1.3 3.6
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 2.3 45.84 17492 929 98.736 0.213 0.2101 0.2101 0.2621 0.2625 RANDOM 41.434
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] 0.12 -0.201 3.812 -3.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.416 r_dihedral_angle_6_deg 14.729 r_lrange_it 10.722 r_dihedral_angle_1_deg 7.99 r_dihedral_angle_2_deg 7.678 r_scangle_it 7.088 r_mcangle_it 6.74 r_scbond_it 4.835 r_mcbond_it 4.352 r_angle_refined_deg 1.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.416 r_dihedral_angle_6_deg 14.729 r_lrange_it 10.722 r_dihedral_angle_1_deg 7.99 r_dihedral_angle_2_deg 7.678 r_scangle_it 7.088 r_mcangle_it 6.74 r_scbond_it 4.835 r_mcbond_it 4.352 r_angle_refined_deg 1.834 r_nbtor_refined 0.314 r_symmetry_nbd_refined 0.23 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.143 r_symmetry_xyhbond_nbd_refined 0.135 r_ncsr_local_group_1 0.127 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2729 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 13
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 PHASER phasing