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E. coli Guanine Deaminase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OOD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Hepes pH 7.5
10% Peg 8000
Crystal Properties Matthews coefficient Solvent content 2.4 48.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.628 α = 104.8 b = 80.588 β = 105.72 c = 101.427 γ = 105.83
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 EIGER X 16M 2017-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9198 APS 24-ID-E
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 2.3 48.91 98 0.088 0.097 0.039 0.998 15 5.7 79427
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.35 96 0.504 0.756 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2OOD 2.3 48.91 75330 3958 97.79 0.2111 0.2086 0.213 0.2582 0.2613 RANDOM 56.557
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] -3.85 1.14 -0.86 1.14 -0.02 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.97 r_dihedral_angle_4_deg 18.426 r_dihedral_angle_3_deg 15.177 r_dihedral_angle_1_deg 7.224 r_angle_refined_deg 1.593 r_angle_other_deg 1.355 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.97 r_dihedral_angle_4_deg 18.426 r_dihedral_angle_3_deg 15.177 r_dihedral_angle_1_deg 7.224 r_angle_refined_deg 1.593 r_angle_other_deg 1.355 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13059 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 16
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing