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Crystal structure of YqeH GTPase from Bacillus anthracis with dGDP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EC1 PDB entry 3EC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.8 298 0.1M Na Citrate pH 5.8, 25% PEG 3350, 4% Isopropanal, 2mM d-GTP, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.26 45.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.13 α = 90 b = 58.99 β = 99.38 c = 77.72 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 CCD MARMOSAIC 300 mm CCD Mirror 2008-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12000 APS 21-ID-D
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 1.8 30 98.4 0.043 19.65 4.09 34009 34009 -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 1.8 1.86 97.7 0.382 3.93 4.13
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 3EC1 1.8 30 32293 1714 98.43 0.21664 0.21524 0.2128 0.2421 0.2416 RANDOM 54.35
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] 1.25 1.64 -2.91 2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.289 r_dihedral_angle_4_deg 11.235 r_dihedral_angle_3_deg 10.966 r_dihedral_angle_1_deg 3.664 r_scangle_it 1.819 r_scbond_it 1.224 r_angle_refined_deg 1.215 r_mcangle_it 0.74 r_mcbond_it 0.471 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.289 r_dihedral_angle_4_deg 11.235 r_dihedral_angle_3_deg 10.966 r_dihedral_angle_1_deg 3.664 r_scangle_it 1.819 r_scbond_it 1.224 r_angle_refined_deg 1.215 r_mcangle_it 0.74 r_mcbond_it 0.471 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.252 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.135 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2417 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 27
Software Software Software Name Purpose BLU-MAX data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling