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Crystal structure of the yeast cytosine deaminase containing both open and closed active sites
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6 295 0.2 M lithium sulfate, 0.1 M MES pH 6.0 and 20% PEG-4000, cryoprotected by the reservoir solution supplemented with 15% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.865 α = 90 b = 40.825 β = 104.79 c = 97.728 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2022-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 1.27899 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.76 94.49 98.8 0.082 0.099 0.038 0.998 12.2 6.6 58759
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.86 99.1 0.883 1.055 0.41 0.736 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.76 52.74 55849 2895 98.66 0.16308 0.16148 0.1723 0.194 0.2002 RANDOM 26.805
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] -0.61 -1.12 0.1 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.765 r_dihedral_angle_3_deg 15.323 r_dihedral_angle_4_deg 14.104 r_long_range_B_refined 6.294 r_dihedral_angle_1_deg 6.259 r_long_range_B_other 6.258 r_scangle_other 5.179 r_scbond_it 3.468 r_scbond_other 3.452 r_mcangle_other 2.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.765 r_dihedral_angle_3_deg 15.323 r_dihedral_angle_4_deg 14.104 r_long_range_B_refined 6.294 r_dihedral_angle_1_deg 6.259 r_long_range_B_other 6.258 r_scangle_other 5.179 r_scbond_it 3.468 r_scbond_other 3.452 r_mcangle_other 2.944 r_mcangle_it 2.943 r_mcbond_it 2.178 r_mcbond_other 2.175 r_angle_refined_deg 1.608 r_angle_other_deg 1.467 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4745 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction MOLREP phasing