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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 8.4 293.15 0.2 M Lithium Citrate tribasic tetrahydrate,
20% PEG 3350,
15% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.35 47.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.229 α = 90 b = 44.241 β = 99.06 c = 90.53 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 PILATUS 6M-F 2025-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92205 Diamond I04-1
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 1.95 45.85 100 0.052 0.061 0.033 0.999 16.7 6.5 28422
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) 1.95 2 100 0.238 0.298 0.177 0.98 4.2 5
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 1.95 44.74 28407 1396 99.979 0.196 0.194 0.194 0.2389 0.239 RANDOM 36.245
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] 2.477 0.217 1.086 -3.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.6 r_dihedral_angle_6_deg 13.949 r_lrange_it 9.38 r_dihedral_angle_1_deg 7.913 r_scangle_it 7.182 r_dihedral_angle_2_deg 6.495 r_scbond_it 5.156 r_mcangle_it 4.983 r_mcbond_it 3.573 r_angle_refined_deg 1.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.6 r_dihedral_angle_6_deg 13.949 r_lrange_it 9.38 r_dihedral_angle_1_deg 7.913 r_scangle_it 7.182 r_dihedral_angle_2_deg 6.495 r_scbond_it 5.156 r_mcangle_it 4.983 r_mcbond_it 3.573 r_angle_refined_deg 1.936 r_nbtor_refined 0.31 r_symmetry_nbd_refined 0.266 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.157 r_symmetry_xyhbond_nbd_refined 0.157 r_ncsr_local_group_1 0.134 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2793 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data reduction gemmi data extraction Aimless data scaling DIALS data reduction gemmi data extraction PHASER phasing