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Crystal structure of Au(10EQ)-apo-R168H/L169C-rHLFr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 Ammonium Sulfate, Cadmium Sulfate
Crystal Properties Matthews coefficient Solvent content 3.17 61.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.126 α = 90 b = 182.126 β = 90 c = 182.126 γ = 90
Symmetry Space Group F 4 3 2
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 RIGAKU HyPix-6000HE 2021-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.540562
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 12.882 99.7 0.038 0.013 1 50.6 9.5 20892
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 0.145 0.058 0.988 12.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1DAT 1.9 12.882 20873 1054 99.443 0.182 0.1807 0.1745 0.2117 0.2027 12.442
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.271 r_dihedral_angle_4_deg 22.167 r_dihedral_angle_3_deg 13.485 r_lrange_it 6.229 r_dihedral_angle_1_deg 5.502 r_scangle_it 3.901 r_scbond_it 2.577 r_mcangle_it 2.442 r_angle_refined_deg 1.825 r_mcbond_it 1.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.271 r_dihedral_angle_4_deg 22.167 r_dihedral_angle_3_deg 13.485 r_lrange_it 6.229 r_dihedral_angle_1_deg 5.502 r_scangle_it 3.901 r_scbond_it 2.577 r_mcangle_it 2.442 r_angle_refined_deg 1.825 r_mcbond_it 1.506 r_metal_ion_refined 0.57 r_symmetry_metal_ion_refined 0.57 r_nbtor_refined 0.311 r_symmetry_nbd_refined 0.244 r_nbd_refined 0.24 r_xyhbond_nbd_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.162 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1368 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Coot model building MOLREP phasing Aimless data scaling