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Structure of thioredoxin (trxA) from Rickettsia prowazekii str. Madrid E.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YJ7 PDB entry 2yj7A as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Rigaku Reagents Precipitant Synergy screen, condition #64: 25% PEG 3350, 15% Propanol-2, 100mM Ammonium-citrate tribasic / citric acid pH 4.5: RiprA.00029.a.A1.PB00094 at 2mg/ml: cryo: direct: puck uwk6-15
Crystal Properties Matthews coefficient Solvent content 1.73 29.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.74 α = 90 b = 45.16 β = 90 c = 60.93 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 CCD RIGAKU SATURN 944+ 2019-01-30 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 1.6 36.281 99.1 0.064 0.066 1 27.99 15.604 12337 20.537
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 1.6 1.64 91.5 0.406 0.45 0.917 3.66 5.186
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 PDB entry 2yj7A as per Morda 1.6 36.281 1.35 12335 1255 99.04 0.1672 0.1628 0.1637 0.206 0.2074 0 18.6506
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 12.507 f_angle_d 0.978 f_chiral_restr 0.057 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 890 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 26
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing Coot model building