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Crystal structure of yeast Thi4-C205S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 295 25% (w/v) PEG1500, 0.0125 M succinic acid, 0.04375M sodium dihydrogen phosphate, and 0.04375M glycine, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.393 α = 90 b = 127.393 β = 90 c = 72.579 γ = 90
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 315 2011-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 40 100 0.07 14.5 5 78765
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 3FPZ 2 38.27 74670 3955 99.72 0.17198 0.17092 0.1714 0.19224 0.1936 RANDOM 23.019
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] -0.39 -0.39 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.57 r_dihedral_angle_4_deg 14.733 r_dihedral_angle_3_deg 13.141 r_dihedral_angle_1_deg 5.789 r_mcangle_it 1.618 r_scangle_it 1.455 r_angle_refined_deg 1.113 r_mcbond_it 0.917 r_scbond_it 0.861 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.57 r_dihedral_angle_4_deg 14.733 r_dihedral_angle_3_deg 13.141 r_dihedral_angle_1_deg 5.789 r_mcangle_it 1.618 r_scangle_it 1.455 r_angle_refined_deg 1.113 r_mcbond_it 0.917 r_scbond_it 0.861 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9080 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing