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Crystal structure of the yeast cytosine deaminase (yCD) M100W mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VLK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8 295 0.2 M lithium chloride, 0.1 M Tris pH 8.0, 20% PEG-6000, cryoprotected by the reservoir solution supplemented with 15% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.839 α = 90 b = 73.07 β = 90 c = 92.82 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 RAYONIX MX-300 2024-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95299 CLSI 08ID-1
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 1.67 46.41 93.7 0.098 0.109 0.048 0.994 9.3 4.8 35226
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 1.67 1.7 62.3 0.492 0.583 0.308 0.729 3.3
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 1.67 41.85 33420 1762 93.27 0.15881 0.15772 0.1683 0.17907 0.1867 RANDOM 18.685
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] -0.43 0.17 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.438 r_dihedral_angle_3_deg 14.226 r_dihedral_angle_4_deg 12.814 r_long_range_B_refined 5.763 r_long_range_B_other 5.657 r_dihedral_angle_1_deg 5.619 r_scangle_other 4.786 r_scbond_it 3.303 r_scbond_other 3.302 r_mcangle_it 2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.438 r_dihedral_angle_3_deg 14.226 r_dihedral_angle_4_deg 12.814 r_long_range_B_refined 5.763 r_long_range_B_other 5.657 r_dihedral_angle_1_deg 5.619 r_scangle_other 4.786 r_scbond_it 3.303 r_scbond_other 3.302 r_mcangle_it 2.43 r_mcangle_other 2.43 r_mcbond_it 1.733 r_mcbond_other 1.733 r_angle_refined_deg 1.653 r_angle_other_deg 1.558 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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 2363 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement Aimless data scaling iMOSFLM data reduction MOLREP phasing