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Crystal structure of Burkholderia pseudomallei effector protein CHBP in complex with ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ PDB ENTRY: 1UBQ AND PDB ENTRY: 3EIR experimental model PDB 3EIR PDB ENTRY: 1UBQ AND PDB ENTRY: 3EIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.2 293 12.5% PEG3350, 125MM MAGNESIUM FORMATE, pH 7.2, EVAPORATION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.431 α = 90 b = 45.185 β = 118.46 c = 67.886 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 120 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 20 95.3 5.7 10218 4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 93.1
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 PDB ENTRY: 1UBQ AND PDB ENTRY: 3EIR 2.6 19.35 9211 1007 95.4 0.222 0.218 0.2169 0.26 0.2564 RANDOM 20.66
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] 0.08 0.05 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.422 r_dihedral_angle_4_deg 16.633 r_dihedral_angle_3_deg 15.506 r_dihedral_angle_1_deg 5.123 r_scangle_it 2.059 r_scbond_it 1.185 r_angle_refined_deg 1.134 r_mcangle_it 0.898 r_mcbond_it 0.477 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.422 r_dihedral_angle_4_deg 16.633 r_dihedral_angle_3_deg 15.506 r_dihedral_angle_1_deg 5.123 r_scangle_it 2.059 r_scbond_it 1.185 r_angle_refined_deg 1.134 r_mcangle_it 0.898 r_mcbond_it 0.477 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2541 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 18
Software Software Software Name Purpose CrystalClear data collection PHASES phasing REFMAC refinement DENZO data reduction