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Fe-Cl bound Y157F CDO at pH ~7.0 in the presence of azide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IEU 4IEU with Cys removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 Purified enzyme was concentrated to ~8 mg/mL and then added into a crystallization screen containing 0.1 M tri-sodium citrate pH=5.6, 24-34% PEG 4K, and 0.1-0.25 M ammonium acetate. 1.5L of protein solution was added to each well and mixed with an equivalent volume of reservoir solution., pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.6 α = 90 b = 57.6 β = 90 c = 122.4 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 100 CCD ADSC QUANTUM 315r 2013-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.3 34 91 27.8 40.7 47533 47060
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 52 1.5 18
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 4IEU with Cys removed 1.3 33.907 1.34 47060 4574 91.3 0.1653 0.1628 0.1743 0.1885 0.1956 same 5% as 4IEU
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 13.184 f_angle_d 1.011 f_chiral_restr 0.083 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1509 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHENIX phasing