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Crystal structure of IrCp* immobilized apo-R52H-rHLFr (25 equiv)
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 Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)
Crystal Properties Matthews coefficient Solvent content 3.19 61.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.995 α = 90 b = 181.995 β = 90 c = 181.995 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 2021-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 19.086 99.3 0.997 12 4.4 41390
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.366
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 1.5 19.086 41378 2062 99.043 0.184 0.1829 0.183 0.2103 0.2105 15.52
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 34.488 r_dihedral_angle_4_deg 20.383 r_dihedral_angle_3_deg 13.141 r_lrange_it 6.525 r_lrange_other 6.148 r_dihedral_angle_1_deg 4.8 r_scangle_it 4.315 r_scangle_other 4.309 r_scbond_it 2.711 r_scbond_other 2.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.488 r_dihedral_angle_4_deg 20.383 r_dihedral_angle_3_deg 13.141 r_lrange_it 6.525 r_lrange_other 6.148 r_dihedral_angle_1_deg 4.8 r_scangle_it 4.315 r_scangle_other 4.309 r_scbond_it 2.711 r_scbond_other 2.701 r_mcangle_it 2.679 r_mcangle_other 2.678 r_angle_refined_deg 1.707 r_mcbond_it 1.657 r_mcbond_other 1.644 r_angle_other_deg 1.577 r_symmetry_metal_ion_refined 0.391 r_metal_ion_refined 0.324 r_xyhbond_nbd_refined 0.278 r_symmetry_nbd_refined 0.277 r_nbd_refined 0.274 r_nbd_other 0.226 r_nbtor_refined 0.179 r_symmetry_nbd_other 0.178 r_symmetry_xyhbond_nbd_other 0.175 r_symmetry_xyhbond_nbd_refined 0.151 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.085 r_xyhbond_nbd_other 0.021 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1384 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing