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Resting state of rat cysteine dioxygenase Y157F variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KWJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 291 Hanging drops of 2.5 microL of approximately 24 mg/mL Y157F-CDO (20mM Tris-Cl pH 8.0) and 2.5 microL reservoir buffer containing seeds from wt-CDO were allowed to equilibrate above the reservoir buffer (26% (w/v) polyethylene glycol 4000, 200 mM ammonium acetate, 100 mM sodium citrate).
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.79 α = 90 b = 57.79 β = 90 c = 121.99 γ = 90
Symmetry Space Group P 43 21 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 CCD ADSC QUANTUM 210r Double Si with sagittaly bent second crystal 2014-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953700 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.81 25.84 100 0.464 0.062 0.997 13.7 55.6 35952 15.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.85 100 0.3592 0.478 0.627 1.8 56.8 1172
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4kwj 1.81 25.84 1.9 35952 1807 99.98 0.1922 0.19 0.2325 0.1901 20.0064
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 f_dihedral_angle_d 13.156 f_angle_d 0.98 f_chiral_restr 0.041 f_bond_d 0.01 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1518 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing