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Crystal structure of a YjeF family protein from Cryptococcus neoformans var. grubii serotype A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Robetta predicted structure from Robetta server
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 285 Optimization screen based on RigakuReagents JCSG+ screen, condition A3: 40% PEG 200, 100mM KH2PO4/Na2HPO4 pH 6.1, 200mM NaCl; CrneC.19313.a.B1.PS38377 at 15mg/ml; cryo: direct; tray 302563a3, puck VLL3-1
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.42 α = 90 b = 85.42 β = 90 c = 187.08 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 RAYONIX MX-300 2018-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.9 36.98 99.8 0.06 0.063 0.999 26.39 11.693 27708 33.281
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 1.9 1.95 98.5 0.538 0.571 0.922 4.29 8.884
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 server 1.9 36.98 1.35 27700 2015 99.83 0.1661 0.1631 0.1646 0.2047 0.2065 0 31.2387
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 15.7 f_angle_d 0.91 f_chiral_restr 0.06 f_bond_d f_plane_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2564 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 6
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing ARP/wARP model building BUCCANEER model building Coot model building