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Crystallographic octamer of a metal-free RIDC1 variant bearing two disulfide bonded cysteines
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 15% 2-methyl-2,4-pentane diol (v/v), 33.3 mM Bis-Tris (pH 6.5), 66.7 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.55 α = 90 b = 78.55 β = 90 c = 168.33 γ = 90
Symmetry Space Group P 41 2 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 2016-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 78.55 99.7 0.088 16.8 9 13669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 99.2 0.469 5.8
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 3IQ6 2.8 78.55 12945 687 99.82 0.21128 0.20805 0.2111 0.27665 0.2716 RANDOM 60.337
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] 1.66 1.66 -3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.036 r_dihedral_angle_3_deg 18.658 r_dihedral_angle_4_deg 11.759 r_long_range_B_refined 9.21 r_long_range_B_other 9.21 r_scangle_other 6.812 r_mcangle_it 6.177 r_mcangle_other 6.175 r_dihedral_angle_1_deg 5.729 r_scbond_it 4.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.036 r_dihedral_angle_3_deg 18.658 r_dihedral_angle_4_deg 11.759 r_long_range_B_refined 9.21 r_long_range_B_other 9.21 r_scangle_other 6.812 r_mcangle_it 6.177 r_mcangle_other 6.175 r_dihedral_angle_1_deg 5.729 r_scbond_it 4.314 r_scbond_other 4.312 r_mcbond_it 4.021 r_mcbond_other 4.015 r_angle_refined_deg 1.589 r_angle_other_deg 1.336 r_chiral_restr 0.121 r_gen_planes_other 0.038 r_bond_other_d 0.032 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 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 3167 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 179
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing