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Crystal structure of apo-R52W/E56W/R59W/E63W-rHLFr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAT 1DAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Ammonium sulphate, Cadmium sulphate
Crystal Properties Matthews coefficient Solvent content 3.09 60.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.133 α = 90 b = 181.133 β = 90 c = 181.133 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 93 PIXEL RIGAKU HyPix-6000HE 2022-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 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 20.259 100 1 25.1 11.8 41179
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 0.947
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 20.259 40827 2068 99.056 0.163 0.1619 0.1618 0.1788 0.1793 11.328
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 37.386 r_dihedral_angle_4_deg 16.172 r_dihedral_angle_3_deg 13.27 r_lrange_it 5.433 r_lrange_other 5.088 r_dihedral_angle_1_deg 4.682 r_scangle_other 3.511 r_scangle_it 3.505 r_scbond_it 2.293 r_scbond_other 2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.386 r_dihedral_angle_4_deg 16.172 r_dihedral_angle_3_deg 13.27 r_lrange_it 5.433 r_lrange_other 5.088 r_dihedral_angle_1_deg 4.682 r_scangle_other 3.511 r_scangle_it 3.505 r_scbond_it 2.293 r_scbond_other 2.28 r_mcangle_it 1.888 r_mcangle_other 1.887 r_angle_refined_deg 1.858 r_angle_other_deg 1.611 r_mcbond_other 1.171 r_mcbond_it 1.17 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.247 r_symmetry_xyhbond_nbd_refined 0.198 r_nbtor_refined 0.187 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.168 r_symmetry_nbd_other 0.161 r_symmetry_metal_ion_refined 0.137 r_chiral_restr 0.101 r_metal_ion_refined 0.097 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.014 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 1393 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing