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Crystal structure of Au(50EQ)-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 60.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.734 α = 90 b = 180.734 β = 90 c = 180.734 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 2021-02-12 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 12.946 99.7 0.085 0.09 0.028 0.999 25.1 9.8 20430
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 0.577 0.622 0.23 0.914
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 1da't 1.9 12.946 20429 1069 99.489 0.17 0.1687 0.1652 0.1951 0.1927 16.91
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 35.391 r_dihedral_angle_4_deg 23.543 r_dihedral_angle_3_deg 14.224 r_lrange_it 7.065 r_dihedral_angle_1_deg 5.347 r_scangle_it 4.677 r_scbond_it 3.146 r_mcangle_it 2.261 r_angle_refined_deg 1.876 r_mcbond_it 1.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.391 r_dihedral_angle_4_deg 23.543 r_dihedral_angle_3_deg 14.224 r_lrange_it 7.065 r_dihedral_angle_1_deg 5.347 r_scangle_it 4.677 r_scbond_it 3.146 r_mcangle_it 2.261 r_angle_refined_deg 1.876 r_mcbond_it 1.551 r_symmetry_metal_ion_refined 0.637 r_metal_ion_refined 0.399 r_nbtor_refined 0.314 r_nbd_refined 0.241 r_symmetry_nbd_refined 0.226 r_xyhbond_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.14 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1363 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building