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Crystal structure of IrCp* immobilized apo-R52H-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 Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)
Crystal Properties Matthews coefficient Solvent content 3.25 62.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.064 α = 90 b = 182.064 β = 90 c = 182.064 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 2019-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.05 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 1.25 45.557 100 0.166 0.168 0.02 1 2.5 73.1 71449
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 1.25 1.27 0.848
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 1.25 41.768 71442 3614 99.985 0.175 0.1746 0.1748 0.1855 0.1859 13.196
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 34.673 r_dihedral_angle_4_deg 18.107 r_dihedral_angle_3_deg 12.383 r_lrange_it 5.784 r_lrange_other 5.499 r_dihedral_angle_1_deg 4.688 r_scangle_it 3.887 r_scangle_other 3.883 r_scbond_it 2.661 r_scbond_other 2.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.673 r_dihedral_angle_4_deg 18.107 r_dihedral_angle_3_deg 12.383 r_lrange_it 5.784 r_lrange_other 5.499 r_dihedral_angle_1_deg 4.688 r_scangle_it 3.887 r_scangle_other 3.883 r_scbond_it 2.661 r_scbond_other 2.606 r_mcangle_it 2.396 r_mcangle_other 2.396 r_angle_refined_deg 2.193 r_angle_other_deg 1.592 r_mcbond_it 1.534 r_mcbond_other 1.51 r_symmetry_metal_ion_refined 0.418 r_symmetry_nbd_refined 0.381 r_metal_ion_refined 0.307 r_nbd_refined 0.295 r_xyhbond_nbd_refined 0.264 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.19 r_nbd_other 0.168 r_symmetry_xyhbond_nbd_refined 0.154 r_chiral_restr 0.118 r_symmetry_nbtor_other 0.095 r_bond_refined_d 0.02 r_symmetry_xyhbond_nbd_other 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1380 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building