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Crystal structure of CheY mutant D53A of Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 289 0.1M sodium acetate, 35% MPEG2000, 0.05M ammonium sulfate, 1mM Magnesium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.778048 30.823023
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.335 α = 90 b = 38.081 β = 107.35 c = 38.639 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2007-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 36.88 98.5 0.082 10.6 3.78 4993 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 97 0.24 4.5 3.82
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3GWG 2.2 15.53 4747 230 98.2 0.1824 0.17986 0.23256 0.2145 RANDOM 14.961
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] 1.57 0.54 -0.73 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.179 r_dihedral_angle_4_deg 21.525 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_1_deg 6.388 r_scangle_it 3.504 r_scbond_it 2.346 r_angle_refined_deg 1.828 r_mcangle_it 1.188 r_mcbond_it 0.645 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.179 r_dihedral_angle_4_deg 21.525 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_1_deg 6.388 r_scangle_it 3.504 r_scbond_it 2.346 r_angle_refined_deg 1.828 r_mcangle_it 1.188 r_mcbond_it 0.645 r_chiral_restr 0.104 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 963 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 11
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling