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Crystal structure of Thioredoxin 1 from Cryptococcus neoformans at 1.8 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 294 1.6 M ammonium sulfate, 0.02 M tris hydrochloride
Crystal Properties Matthews coefficient Solvent content 3.34 63.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.706 α = 90 b = 110.706 β = 90 c = 91.763 γ = 120
Symmetry Space Group P 64 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 MARMOSAIC 225 mm CCD 2015-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.2398 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 25 100 0.092 52.9 37.1 31224
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 100 0.581 6.2 34.7
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 2J23 1.8 95.87 29599 1542 99.73 0.15826 0.15634 0.1696 0.19549 0.2012 RANDOM 37.274
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] -0.9 -0.45 -0.9 2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.487 r_dihedral_angle_3_deg 14.354 r_long_range_B_refined 8.52 r_long_range_B_other 8.275 r_dihedral_angle_1_deg 5.607 r_scangle_other 4.659 r_scbond_it 3.137 r_scbond_other 3.081 r_mcangle_it 2.324 r_mcangle_other 2.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.487 r_dihedral_angle_3_deg 14.354 r_long_range_B_refined 8.52 r_long_range_B_other 8.275 r_dihedral_angle_1_deg 5.607 r_scangle_other 4.659 r_scbond_it 3.137 r_scbond_other 3.081 r_mcangle_it 2.324 r_mcangle_other 2.323 r_angle_refined_deg 2.189 r_mcbond_it 1.708 r_mcbond_other 1.675 r_angle_other_deg 1.139 r_chiral_restr 0.145 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1632 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing