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Crystal structure of an antigenic nucleotidyltransferase-like protein from Paracoccidioides brasiliensis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.25 M MgCl2, 25% PEG 4000, 0.1 M Tris-HCl pH 7.0 - 8,0 2 VAPOR DIFFUSION, HANGING DROP 293.15 0.25 M MgCl2, 25% PEG 4000, 0.1 M Tris-HCl pH 7.0 - 8,0
Crystal was incubated in a cryo-soaking solution containing 100 mM NaI and 10% (v/v) ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.1 41.5 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.649 α = 90 b = 51.105 β = 90 c = 121.19 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 2M collimating mirror and toroidal bendable mirror 2013-05-24 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MAR CCD 165 mm collimating mirror and toroidal bendable mirror 2014-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4587 LNLS W01B-MX2 2 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4587 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 2 1.68 31.77 86.1 0.039 18.5 1.9 39751 -3 22.5
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) 2 1.68 1.71 68.9 0.172 3.7 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.86 47.09 16999 895 97.85 0.16216 0.15909 0.1709 0.22168 0.2318 RANDOM 17.673
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] -0.93 2.25 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.061 r_dihedral_angle_4_deg 20.954 r_dihedral_angle_3_deg 13.741 r_long_range_B_refined 5.573 r_dihedral_angle_1_deg 5.236 r_long_range_B_other 5.236 r_scangle_other 3.578 r_scbond_it 2.308 r_scbond_other 2.308 r_mcangle_other 1.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.061 r_dihedral_angle_4_deg 20.954 r_dihedral_angle_3_deg 13.741 r_long_range_B_refined 5.573 r_dihedral_angle_1_deg 5.236 r_long_range_B_other 5.236 r_scangle_other 3.578 r_scbond_it 2.308 r_scbond_other 2.308 r_mcangle_other 1.909 r_mcangle_it 1.908 r_angle_refined_deg 1.878 r_mcbond_it 1.338 r_mcbond_other 1.325 r_angle_other_deg 1.075 r_chiral_restr 0.111 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 1718 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data processing DENZO data processing XDS data scaling HKL-2000 data scaling AutoSol phasing