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Cryptococcus neoformans AIR synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1 M SPG (succinic acid, sodium dihydrogen phosphate, and glycine in ratio of 2:7:7), 25% w/v PEG1500
Crystal Properties Matthews coefficient Solvent content 1.9 35.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.3 α = 90 b = 85.769 β = 91.698 c = 37.018 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2018-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.24 42.88 99.7 0.078 0.092 0.999 0.148 6.9 12876 37.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.24 2.31 96.8 0.693 0.823 0.848 0.026 6.6
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 5VK4 2.24 42.88 1.35 12869 552 99.64 0.1983 0.1965 0.197 0.237 0.2383 46.71
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 9.6326 f_angle_d 0.4206 f_chiral_restr 0.0415 f_plane_restr 0.0027 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2103 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection XDS data reduction Aimless data scaling PHASER phasing Coot model building