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Cyanophage S-2L Succinoaminodeoxyadenylate synthetase (PurZ) bound to dGMP and dATP as an energy donor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277.15 15% v/v Tacsimate; 2% w/v PEG 3350; 100 mM HEPES pH 7
Crystal Properties Matthews coefficient Solvent content 3.01 59.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.18 α = 90 b = 108.18 β = 90 c = 142.33 γ = 120
Symmetry Space Group P 62 2 2
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 9M KB Mirrors 2019-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980130 SOLEIL PROXIMA 2
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 1.69617086092 44.5 99.8 0.081 0.082 0.013 1 34.1 39.6 54836 28.6904003452
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 1.7 1.74 98 2.661 2.695 0.419 0.694 1.7 39.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6FM1 1.69617086092 44.4954227156 1.33794450571 54761 2738 99.7104879825 0.160215360219 0.159386977715 0.1618 0.17601031371 0.1806 32.2959699757
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 26.4579568102 f_angle_d 1.00436889056 f_chiral_restr 0.0678462690405 f_bond_d 0.00959554207283 f_plane_restr 0.00535924337827
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2691 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing