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Crystal structure of Au(200EQ)-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 3.19 61.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.594 α = 90 b = 182.594 β = 90 c = 182.594 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 DECTRIS PILATUS 6M 2019-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00 SPring-8 BL45XU
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 1.85 45.69 100 0.07 0.099 0.07 0.856 9.1 1.8 22847
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 1.85 1.89 0.075 0.106 0.075 0.978 1.9
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 1.85 45.69 22823 1116 99.886 0.168 0.1662 0.1718 0.198 0.1999 13.278
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 33.944 r_dihedral_angle_4_deg 22.88 r_dihedral_angle_3_deg 13.518 r_lrange_it 5.765 r_dihedral_angle_1_deg 5.272 r_scangle_it 4.351 r_scbond_it 2.788 r_mcangle_it 1.815 r_angle_refined_deg 1.788 r_mcbond_it 1.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.944 r_dihedral_angle_4_deg 22.88 r_dihedral_angle_3_deg 13.518 r_lrange_it 5.765 r_dihedral_angle_1_deg 5.272 r_scangle_it 4.351 r_scbond_it 2.788 r_mcangle_it 1.815 r_angle_refined_deg 1.788 r_mcbond_it 1.295 r_symmetry_metal_ion_refined 0.342 r_nbtor_refined 0.306 r_symmetry_nbd_refined 0.274 r_metal_ion_refined 0.253 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.115 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1363 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Aimless data scaling MOLREP phasing Coot model building