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Crystal structure of Au(100EQ)-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 3.07 59.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.213 α = 90 b = 180.213 β = 90 c = 180.213 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 2021-02-07 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 12.91 99.7 0.091 0.096 0.03 0.998 21.5 9.5 20252
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 0.557 0.606 0.237 0.877 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1dat 1.9 12.909 20250 991 99.489 0.172 0.17 0.1671 0.2085 0.2028 16.605
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 33.588 r_dihedral_angle_4_deg 21.441 r_dihedral_angle_3_deg 14.546 r_lrange_it 6.117 r_dihedral_angle_1_deg 5.212 r_scangle_it 4.454 r_scbond_it 2.975 r_mcangle_it 2.315 r_angle_refined_deg 1.775 r_mcbond_it 1.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.588 r_dihedral_angle_4_deg 21.441 r_dihedral_angle_3_deg 14.546 r_lrange_it 6.117 r_dihedral_angle_1_deg 5.212 r_scangle_it 4.454 r_scbond_it 2.975 r_mcangle_it 2.315 r_angle_refined_deg 1.775 r_mcbond_it 1.602 r_nbtor_refined 0.311 r_symmetry_nbd_refined 0.232 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.2 r_symmetry_xyhbond_nbd_refined 0.179 r_chiral_restr 0.106 r_metal_ion_refined 0.095 r_symmetry_metal_ion_refined 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1363 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building