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1.76 Angstrom Crystal Structure of GTP-binding Protein Der from Coxiella burnetii in Complex with GDP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 Protein: 11.0 mg/ml, 0.25M Sodium chloride, 0.01M Tris-HCl pH 8.3, 10mM GDP, Screen: JSCG+ (H11), 0.2M Magnesium chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.37 48.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.275 α = 90 b = 98.443 β = 90 c = 107.968 γ = 90
Symmetry Space Group P 21 21 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 325 mm CCD 2014-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.76 30 99.7 0.051 0.051 33.8 7.2 47308 -3
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 1.76 1.79 100 0.537 3.9 7.3
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 2HJC 1.76 29.05 44856 2386 99.21 0.17295 0.17128 0.1815 0.2044 0.2087 RANDOM 39.181
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] 0.61 -0.85 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.989 r_dihedral_angle_4_deg 12.319 r_dihedral_angle_3_deg 10.239 r_long_range_B_refined 7.467 r_long_range_B_other 7.342 r_scangle_other 4.476 r_mcangle_it 3.218 r_dihedral_angle_1_deg 3.217 r_mcangle_other 3.217 r_scbond_other 2.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.989 r_dihedral_angle_4_deg 12.319 r_dihedral_angle_3_deg 10.239 r_long_range_B_refined 7.467 r_long_range_B_other 7.342 r_scangle_other 4.476 r_mcangle_it 3.218 r_dihedral_angle_1_deg 3.217 r_mcangle_other 3.217 r_scbond_other 2.816 r_scbond_it 2.812 r_mcbond_it 2.114 r_mcbond_other 2.108 r_angle_refined_deg 1.473 r_angle_other_deg 0.746 r_chiral_restr 0.084 r_gen_planes_refined 0.02 r_gen_planes_other 0.016 r_bond_refined_d 0.009 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3187 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-2000 data scaling PHASER phasing HKL-2000 data reduction