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Yeast Cytosine Deaminase mutant-M100H
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 VAPOR DIFFUSION, HANGING DROP 277.15 0.1M sodium cacodylate, 0.16M sodium acetate, 24% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.077 α = 90 b = 79.077 β = 90 c = 55.91 γ = 90
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 MX300HE 2020-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.439 50 99.8 0.025 31.3 11.4 62709
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.49 98.4 0.122
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.439 27.958 62481 3090 99.743 0.128 0.1272 0.127 0.1442 0.1446 14.027
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] 0.041 0.041 -0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.016 r_dihedral_angle_3_deg 13.467 r_lrange_it 10.33 r_lrange_other 9.048 r_dihedral_angle_2_deg 6.906 r_scangle_it 6.392 r_scangle_other 6.39 r_dihedral_angle_1_deg 5.573 r_scbond_it 4.242 r_scbond_other 4.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.016 r_dihedral_angle_3_deg 13.467 r_lrange_it 10.33 r_lrange_other 9.048 r_dihedral_angle_2_deg 6.906 r_scangle_it 6.392 r_scangle_other 6.39 r_dihedral_angle_1_deg 5.573 r_scbond_it 4.242 r_scbond_other 4.209 r_mcangle_it 3.738 r_mcangle_other 3.738 r_mcbond_it 2.494 r_mcbond_other 2.489 r_rigid_bond_restr 2.48 r_angle_refined_deg 1.326 r_angle_other_deg 0.465 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.216 r_metal_ion_refined 0.199 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.165 r_nbd_other 0.138 r_xyhbond_nbd_refined 0.108 r_symmetry_nbtor_other 0.077 r_ncsr_local_group_1 0.073 r_chiral_restr 0.072 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2370 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling PHASER phasing