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Crystal structure of Chey mutant T84A 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 1.792501 31.380779
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.409 α = 90 b = 38.062 β = 107.58 c = 39.02 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 2008-04-07 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 1.7 23.08 99.9 0.033 14.2 3.48 10972 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) 1.7 1.76 0.199 5.2 3.34
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 1.7 17.39 10437 527 99.81 0.17495 0.17351 0.1742 0.20281 0.2032 RANDOM 9.239
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] -0.1 -0.13 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.419 r_dihedral_angle_4_deg 20.374 r_dihedral_angle_3_deg 11.189 r_dihedral_angle_1_deg 5.187 r_scangle_it 3.675 r_scbond_it 2.258 r_angle_refined_deg 1.418 r_mcangle_it 1.187 r_mcbond_it 0.68 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.419 r_dihedral_angle_4_deg 20.374 r_dihedral_angle_3_deg 11.189 r_dihedral_angle_1_deg 5.187 r_scangle_it 3.675 r_scbond_it 2.258 r_angle_refined_deg 1.418 r_mcangle_it 1.187 r_mcbond_it 0.68 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 964 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 12
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling