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Crystal structure of a YjeF family protein from Cryptococcus neoformans var. grubii serotype A in complex with AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Robetta predicted structure from Robetta
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 285 Optimization screen based on RigakuReagents JCSG+ screen, condition D3: 49% PEG 200, 100mM KH2PO4/Na2HPO4 pH 5.7, 100mM NaCl: CrneC.19313.a.B1.PS38377 at 15mg/ml + 2.5mM MgCl2 + 2.5mM AMPPNP: cryo: 10% EG + compounds: tray 301295g1, puck HWU2-5
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.34 α = 90 b = 85.34 β = 90 c = 187.93 γ = 90
Symmetry Space Group I 4 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 CCD RIGAKU SATURN 944+ 2018-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 46.982 99.9 0.078 0.081 0.999 22.84 10.728 23914 31.002
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 2.05 99.9 0.574 0.62 0.889 3.41 7.046
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT predicted structure from Robetta 2 46.982 1.34 23905 1921 99.86 0.1675 0.1637 0.1653 0.2108 0.2128 0 29.4625
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 16 f_angle_d 0.93 f_chiral_restr 0.06 f_bond_d f_plane_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2540 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing BUCCANEER model building ARP/wARP model building Coot model building