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Crystal structure of Fe(III)-bound YtgA from Chlamydia trachomatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 22 % (w/v) polyethylene glycol (PEG) 6000, 0.2 M CaCl2, 0.01 M FeCl3 and 0.1 M MES, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.35 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.841 α = 90 b = 61.072 β = 96.945 c = 105.5 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 210r 2014-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.954 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 19.08 100 0.09 0.04 0.99 16.51 7.3 20476 29.9512762463
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 98.9 0.99 0.39 0.734 2.03 7.2
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 FREE R-VALUE 1PSZ 2.00006345565 19.076725379 1.38024537978 20467 990 99.8438948241 0.181851425707 0.179516182994 0.1797 0.225204578609 0.2247 random selection 39.1926758415
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 20.6194983044 f_angle_d 0.941622931674 f_chiral_restr 0.063689897835 f_bond_d 0.00848462179349 f_plane_restr 0.00506352086264
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2278 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX model building PHENIX refinement