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P46, an immunodominant surface protein from Mycoplasma hyopneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YWH 4YWH, 3URM, 4WWH experimental model PDB 3URM 4YWH, 3URM, 4WWH experimental model PDB 4WWH 4YWH, 3URM, 4WWH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M Tris pH 8.5
0.2 M Sodium Acetate
32% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.87 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.478 α = 90 b = 136.478 β = 90 c = 139.132 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS3 S 6M 2017-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.000 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.1 58.9 97.59 0.97 22.88 10.56 26816 85.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.2 0.17 1.9
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 4YWH, 3URM, 4WWH 3.1 54.39 1.34 26739 1380 96.88 0.2057 0.2033 0.2121 0.2486 0.2503 87.85
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 15.9337 f_angle_d 0.6492 f_chiral_restr 0.048 f_plane_restr 0.0042 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8580 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement PHENIX refinement MOSFLM data reduction SCALA data scaling MOLREP phasing