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Structure of IrCp* immobilized apo-D38H-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 3.19 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.937 α = 90 b = 181.937 β = 90 c = 181.937 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) 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 45.526 100 0.2 0.999 23.1 72.5 71305
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 0.82 2.5
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 41.739 71303 3571 99.989 0.172 0.1714 0.1717 0.1828 0.1825 14.399
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 34.339 r_dihedral_angle_4_deg 18.42 r_dihedral_angle_3_deg 13.427 r_lrange_it 5.98 r_lrange_other 5.704 r_dihedral_angle_1_deg 4.654 r_scangle_it 3.98 r_scangle_other 3.964 r_scbond_it 2.695 r_scbond_other 2.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_4_deg 18.42 r_dihedral_angle_3_deg 13.427 r_lrange_it 5.98 r_lrange_other 5.704 r_dihedral_angle_1_deg 4.654 r_scangle_it 3.98 r_scangle_other 3.964 r_scbond_it 2.695 r_scbond_other 2.611 r_mcangle_it 2.293 r_mcangle_other 2.292 r_angle_refined_deg 2.201 r_angle_other_deg 1.581 r_mcbond_it 1.49 r_mcbond_other 1.482 r_symmetry_metal_ion_refined 0.41 r_symmetry_nbd_refined 0.33 r_metal_ion_refined 0.312 r_nbd_refined 0.293 r_xyhbond_nbd_refined 0.249 r_nbd_other 0.205 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.17 r_chiral_restr 0.124 r_symmetry_nbtor_other 0.097 r_bond_refined_d 0.02 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 1381 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building