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Crystal Structure of a Putative Cysteine Dioxygenase From Bacillus subtilis with Cys-bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EQE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 Purified enzyme was concentrated to 10 mg/mL and 4 uL was mixed with 4 uL of a reservoir containing 18% (w/v) PEG 4000, 0.1 M potassium acetate, 0.05 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.73 54.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.53 α = 90 b = 65.53 β = 90 c = 199.36 γ = 90
Symmetry Space Group P 43 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 CCD ADSC QUANTUM 315r 2013-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.976 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 50 100 0.186 0.038 13.4 23.4 20271 20271
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 2.892 0.767 1 13.7 1939
Refinement Statistics Diffraction ID Structure Solution 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 MOLECULAR REPLACEMENT 3eqe 2.3 46.66 1.33 20197 849 99.91 0.193 0.1902 0.1986 0.2623 0.2677 same as 3eqe, random 5 % beyond 2.82 Ang
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 14.272 f_angle_d 1.06 f_chiral_restr 0.039 f_bond_d 0.012 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2349 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 16
Software Software Software Name Purpose ADSC data collection PHENIX model building PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing