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Crystal Structure of an Uncharacterized Protein (Rv0315 ortholog) from Mycobacterium paratuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 290 JCSG+(c1): 20% PEG-8000, 100mM Sodium phosphate dibasic/ citric acid, pH=4.2, 200mM Sodium Chloride mixed with MypaA.18623.a.B2.PS01983 at 26.32 mg/ml, tray 252788c1258195b4
Crystal Properties Matthews coefficient Solvent content 1.75 29.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.03 α = 90 b = 49.53 β = 95.21 c = 55.31 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 944+ 2014-12-31 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) 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 50 94.8 0.045 0.046 35.5 12 24420 -3 10.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 83.5 0.21 0.225 8.04 7.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4PQ9 1.6 36.83 1.35 24420 2068 94.83 0.1427 0.1401 0.1422 0.1706 0.1719 13.5548
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 12.408 f_angle_d 1.157 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 1635 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction BALBES phasing