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Crystal structure of Au(400EQ)-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 3.1 60.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.889 α = 90 b = 180.889 β = 90 c = 180.889 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) 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 1.9 12.957 99.7 0.142 0.149 0.046 0.996 17.7 10.2 20431
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 1.9 1.94 100 0.651 0.698 0.249 0.874 3.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1dat 1.9 12.957 19840 1038 96.362 0.185 0.1831 0.217 0.2331 17.355
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 34.32 r_dihedral_angle_4_deg 20.656 r_dihedral_angle_3_deg 14.115 r_lrange_it 6.492 r_dihedral_angle_1_deg 5.28 r_scangle_it 3.815 r_scbond_it 2.52 r_mcangle_it 2.239 r_angle_refined_deg 1.678 r_mcbond_it 1.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.32 r_dihedral_angle_4_deg 20.656 r_dihedral_angle_3_deg 14.115 r_lrange_it 6.492 r_dihedral_angle_1_deg 5.28 r_scangle_it 3.815 r_scbond_it 2.52 r_mcangle_it 2.239 r_angle_refined_deg 1.678 r_mcbond_it 1.432 r_nbtor_refined 0.309 r_symmetry_xyhbond_nbd_refined 0.267 r_xyhbond_nbd_refined 0.266 r_symmetry_nbd_refined 0.26 r_symmetry_metal_ion_refined 0.237 r_nbd_refined 0.223 r_metal_ion_refined 0.133 r_chiral_restr 0.109 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1362 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building