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Crystal Structure of Human LanCL1 complexed with GSH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E6U PDB ENTRY 3E6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 1.5M ammonium formate, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 7.062088 82.583054
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.1 α = 90 b = 194.101 β = 90 c = 243.554 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2007-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.8 49.33 88.4 59222
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.873 64.5
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 PDB ENTRY 3E6U 2.8 49.33 56848 2374 88.4 0.23272 0.23147 0.2275 0.26244 0.2576 RANDOM 89.306
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] 0.13 0.06 0.13 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.78 r_dihedral_angle_3_deg 21.018 r_dihedral_angle_4_deg 17.962 r_dihedral_angle_1_deg 6.201 r_scangle_it 1.385 r_angle_refined_deg 1.33 r_mcangle_it 0.839 r_scbond_it 0.752 r_mcbond_it 0.448 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.78 r_dihedral_angle_3_deg 21.018 r_dihedral_angle_4_deg 17.962 r_dihedral_angle_1_deg 6.201 r_scangle_it 1.385 r_angle_refined_deg 1.33 r_mcangle_it 0.839 r_scbond_it 0.752 r_mcbond_it 0.448 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6436 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing