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Crystal structure of 5-methylcytosine deaminase from Klebsiella pneumoniae liganded with 5-fluorocytosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JNR PDB entry 4JNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 30% PEG 4000, 0.1M SODIUM CITRATE, 0.2M AMMONIUM ACETATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.954 α = 90 b = 162.419 β = 90 c = 184.047 γ = 90
Symmetry Space Group P 21 21 21
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 2013-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 1.952 46.663 95.41 211096
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 4JNR 1.952 46.663 211096 6377 95.41 0.1657 0.1646 0.166 0.2008 0.2018
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 14.088 f_angle_d 1.057 f_chiral_restr 0.071 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19320 Nucleic Acid Atoms Solvent Atoms 1148 Heterogen Atoms 295
Software Software Software Name Purpose CBASS data collection BALBES phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling