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Crystal Structure of the N-terminal Fic Domain of a Putative Cell Filamentation protein (VirB-translocated Bep effector protein) with bound ADP from Bartonella quintana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JK8 pdb entry 2JK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 JCSG+(g7): 01.M Succinic Acid, pH=7.0, 15% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.39 48.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.45 α = 90 b = 64.07 β = 90 c = 97.6 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 225 mm CCD Beryllium Lenses 2013-10-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9786 APS 21-ID-F
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 1.55 50 99.6 0.046 22.71 6 37687 37518 -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 1.55 1.59 99.3 0.49 3.51
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2JK8 1.55 19.88 39325 35577 1874 99.54 0.17326 0.17214 0.1782 0.19419 0.1931 RANDOM 22.704
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] 0.18 0.05 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.111 r_dihedral_angle_4_deg 17.835 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_1_deg 4.793 r_mcangle_it 1.581 r_angle_refined_deg 1.491 r_scbond_it 1.431 r_mcbond_it 0.931 r_mcbond_other 0.931 r_angle_other_deg 0.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.111 r_dihedral_angle_4_deg 17.835 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_1_deg 4.793 r_mcangle_it 1.581 r_angle_refined_deg 1.491 r_scbond_it 1.431 r_mcbond_it 0.931 r_mcbond_other 0.931 r_angle_other_deg 0.782 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1695 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 28
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection