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Crystal Structure of Bifunctional protein FolD from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P2O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Tray 291037 Morpheus A3: 10% w/v PEG 4000, 20% v/v glycerol 0.03 M of each divalent cation (0.3 M magnesium chloride, 0.3 M calcium chloride) 0.1 M MES/imidazole pH 6.5
: cryo: direct: HepyC.00934.a.B1 PS38251 at 20 mg/ml, puck mxk4-8
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.88 α = 90 b = 109.04 β = 90 c = 83.8 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 225 mm CCD Beryllium Lenses 2017-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.45 33.222 99.9 0.035 0.037 1 28.34 7.194 56895 -3 17.4
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 1.45 1.49 100 0.421 0.454 0.935 4.19 7.178
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3p2o 1.45 33.222 1.35 56863 1962 99.91 0.1675 0.1669 0.1824 0.1922 25.3501
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 14.968 f_angle_d 0.794 f_chiral_restr 0.075 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2135 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 26
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MOLREP phasing