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GSTM1 in complex with bithionol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Amino acids, 0.1 M MES pH 6.0 - 7.0, 40%-50% Mix1 (Mix1: 40% v/v PEG550*MME, 20% w/v PEG20000)
Crystal Properties Matthews coefficient Solvent content 2.36 47.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.209 α = 90 b = 212.239 β = 95.82 c = 91.645 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 PILATUS3 6M 2023-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9792 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.49 45.63 98.3 0.17 0.116 7.03 2.9 65334
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 2.5 2.54 0.402
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 (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 2.5 45.63 61656 3265 98.84 0.23942 0.23797 0.2388 0.26664 0.2658 RANDOM 65.386
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] 2.2 -3.48 -0.97 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.807 r_long_range_B_refined 5.504 r_long_range_B_other 5.496 r_dihedral_angle_1_deg 5.358 r_dihedral_angle_2_deg 4.636 r_mcangle_it 3.273 r_mcangle_other 3.273 r_scangle_other 3.028 r_mcbond_it 1.884 r_mcbond_other 1.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.807 r_long_range_B_refined 5.504 r_long_range_B_other 5.496 r_dihedral_angle_1_deg 5.358 r_dihedral_angle_2_deg 4.636 r_mcangle_it 3.273 r_mcangle_other 3.273 r_scangle_other 3.028 r_mcbond_it 1.884 r_mcbond_other 1.884 r_scbond_it 1.76 r_scbond_other 1.759 r_angle_refined_deg 1 r_angle_other_deg 0.373 r_chiral_restr 0.053 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 14496 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing