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Crystal structure of apo-R168C/L169C-Fr
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 sulphate, Cadmium sulphate
Crystal Properties Matthews coefficient Solvent content 3.15 60.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.606 α = 90 b = 181.606 β = 90 c = 181.606 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 CCD ADSC QUANTUM 210 2018-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.58 30.01 99.5 0.076 61.9 9.2 35456
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.61 0.246
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DAT 1.58 27.71 33626 1821 99.42 0.16779 0.16704 0.1817 0.18186 0.1945 RANDOM 15.799
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 31.947 r_dihedral_angle_4_deg 19.633 r_dihedral_angle_3_deg 13.066 r_long_range_B_refined 5.482 r_long_range_B_other 5.33 r_dihedral_angle_1_deg 4.896 r_scangle_other 4.74 r_scbond_it 3.092 r_scbond_other 3.079 r_mcangle_other 2.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.947 r_dihedral_angle_4_deg 19.633 r_dihedral_angle_3_deg 13.066 r_long_range_B_refined 5.482 r_long_range_B_other 5.33 r_dihedral_angle_1_deg 4.896 r_scangle_other 4.74 r_scbond_it 3.092 r_scbond_other 3.079 r_mcangle_other 2.501 r_mcangle_it 2.498 r_angle_refined_deg 1.882 r_mcbond_it 1.763 r_mcbond_other 1.748 r_angle_other_deg 1.626 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1360 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing