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Human LanCL1 C264A mutant bound to GSH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 282.15 0.70-0.75 M succinic acid pH 7.0, 0.1 M bis-tris-propane pH 7.0.
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.587 α = 90 b = 120.257 β = 90 c = 143.019 γ = 90
Symmetry Space Group P 21 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 9M 2021-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12723 APS 21-ID-D
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 1.786 92.043 99.3 0.099 0.105 0.034 0.999 13.5 9.5 90992
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 1.786 1.792 93.7 1.083 1.158 0.393 0.879 2.1 8.2
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 3E6U 1.79 25 85974 4469 99.24 0.18247 0.18145 0.1833 0.20186 0.2034 RANDOM 29.95
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] -2.26 4.7 -2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.372 r_dihedral_angle_4_deg 20.794 r_dihedral_angle_3_deg 15.253 r_dihedral_angle_1_deg 6.389 r_long_range_B_refined 5.321 r_scbond_it 2.631 r_mcangle_it 2.298 r_mcbond_it 1.564 r_angle_refined_deg 1.215 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.372 r_dihedral_angle_4_deg 20.794 r_dihedral_angle_3_deg 15.253 r_dihedral_angle_1_deg 6.389 r_long_range_B_refined 5.321 r_scbond_it 2.631 r_mcangle_it 2.298 r_mcbond_it 1.564 r_angle_refined_deg 1.215 r_chiral_restr 0.098 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6404 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction Aimless data scaling PHASER phasing