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Human LanCL1 bound to GSH and Dhb-Erk peptide
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 7 282 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 53.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.688 α = 90 b = 120.562 β = 90 c = 144.224 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 CCD RAYONIX MX-300 2021-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97856 APS 21-ID-F
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 1.91 92.5 100 0.119 0.126 0.041 0.998 13.5 10 75709
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 1.914 1.92 100 1.284 1.36 0.438 0.785 2.1 10.1
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 1.91 25 71871 3759 99.85 0.18542 0.184 0.1867 0.21338 0.2154 RANDOM 31.31
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] 0.53 2.87 -3.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.254 r_dihedral_angle_4_deg 15.782 r_dihedral_angle_3_deg 14.257 r_dihedral_angle_1_deg 6.297 r_long_range_B_refined 5.48 r_mcangle_it 2.185 r_scbond_it 2.115 r_mcbond_it 1.416 r_angle_refined_deg 1.079 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.254 r_dihedral_angle_4_deg 15.782 r_dihedral_angle_3_deg 14.257 r_dihedral_angle_1_deg 6.297 r_long_range_B_refined 5.48 r_mcangle_it 2.185 r_scbond_it 2.115 r_mcbond_it 1.416 r_angle_refined_deg 1.079 r_chiral_restr 0.094 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 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 6452 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction Aimless data scaling PHASER phasing