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Crystal structure of Mg(2+) and BeH(3)(-)-bound CheY 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, 1:10 beryllium, 1:100 sodium fluoride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.778725 30.849339
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.956 α = 90 b = 38.098 β = 106.95 c = 38.885 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 2007-11-21 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 33.32 95.3 0.019 55.1 4.27 4888 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 91.8 0.029 39 4.36
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3GWG 2.4 33.32 3613 167 96.33 0.15449 0.15137 0.2194 0.22013 0.1767 RANDOM 6.273
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] 0.07 0.05 0.14 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39 r_dihedral_angle_4_deg 20.323 r_dihedral_angle_3_deg 14.085 r_dihedral_angle_1_deg 5.237 r_scangle_it 2.524 r_angle_other_deg 2.43 r_scbond_it 1.543 r_angle_refined_deg 1.395 r_mcangle_it 0.926 r_mcbond_it 0.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39 r_dihedral_angle_4_deg 20.323 r_dihedral_angle_3_deg 14.085 r_dihedral_angle_1_deg 5.237 r_scangle_it 2.524 r_angle_other_deg 2.43 r_scbond_it 1.543 r_angle_refined_deg 1.395 r_mcangle_it 0.926 r_mcbond_it 0.481 r_mcbond_other 0.098 r_chiral_restr 0.067 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 966 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 11
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling