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The crystal structure of yeast cytosine deaminase bound to 4(R)-hydroxyl-3,4-dihydropyrimidine at 1.14 angstroms.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microseeding 6.5 277 PEG 8000, calcium acetate, sodium cacodylate, pH 6.5, microseeding, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.66 35.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.88 α = 90 b = 70.417 β = 90 c = 71.523 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 210 2002-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.14 20 92.7 0.048 20.84 92236 92236
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.14 1.18 61.6 0.283 3.81
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R 1OX7 1.14 10 92220 92220 4589 92.7 0.1121 0.1097 0.1097 0.1521 0.1325 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 16 1986.52 2903.5
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.103 s_non_zero_chiral_vol 0.083 s_zero_chiral_vol 0.071 s_anti_bump_dis_restr 0.042 s_similar_adp_cmpnt 0.032 s_angle_d 0.029 s_from_restr_planes 0.0274 s_bond_d 0.011 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2507 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 20
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing