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Pyrococcus horikoshii CoA Disulfide Reductase Quadruple Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FX9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.7 298 5-100 mM sodium acetate, pH 4.7, 50-100 mM ammonium acetate, 4-8% PEG 8000, and 0.01% sodium azide
Crystal Properties Matthews coefficient Solvent content 2.73 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.965 α = 90 b = 191.965 β = 90 c = 74.866 γ = 120
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 2013-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.98 SSRL BL12-2
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 3.6 95.98 99.4 0.041 22.8 5.2 11879
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 3.6 3.73 96.8 0.466 3 4.8
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 4FX9 3.6 95.98 11302 575 99.6 0.24719 0.24508 0.2562 0.28984 0.2877 RANDOM 180.276
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] -17.06 -8.53 -17.06 55.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.129 r_long_range_B_refined 20.652 r_long_range_B_other 20.651 r_dihedral_angle_3_deg 19.015 r_dihedral_angle_4_deg 15.809 r_scangle_other 12.805 r_mcangle_it 12.561 r_mcangle_other 12.56 r_scbond_it 7.742 r_scbond_other 7.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.129 r_long_range_B_refined 20.652 r_long_range_B_other 20.651 r_dihedral_angle_3_deg 19.015 r_dihedral_angle_4_deg 15.809 r_scangle_other 12.805 r_mcangle_it 12.561 r_mcangle_other 12.56 r_scbond_it 7.742 r_scbond_other 7.741 r_mcbond_it 7.431 r_mcbond_other 7.43 r_dihedral_angle_1_deg 6.385 r_angle_refined_deg 1.756 r_angle_other_deg 1.349 r_chiral_restr 0.138 r_bond_other_d 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 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 6821 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing