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Crystal Structure of the N-terminal FIC domain of Bep8 protein (VirB-translocated Bartonella effector protein) from Bartonella sp. 1-1C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NPS pdb entry 4NPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 JCSG+(f12): 30% Jeffamine M-600, pH=7.0, 100mM HEPES free acid/ NaOH, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.6 52.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.81 α = 90 b = 324.16 β = 109.24 c = 86.13 γ = 90
Symmetry Space Group P 1 21 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 225 mm CCD Beryllium Lenses 2014-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97857 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 2.35 50 99 0.08 13.28 3.7 119584 118369 -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 2.35 2.41 99.2 0.569 2.4
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 4NPS 2.35 50 124036 112574 5731 99.1 0.24273 0.24191 0.2408 0.25873 0.2555 RANDOM 48.131
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] 0.13 1.61 -4.66 2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.47 r_dihedral_angle_4_deg 15.541 r_dihedral_angle_3_deg 14.677 r_dihedral_angle_1_deg 4.536 r_angle_other_deg 1.407 r_mcangle_it 1.301 r_angle_refined_deg 1.244 r_mcbond_it 0.735 r_mcbond_other 0.734 r_scbond_it 0.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.47 r_dihedral_angle_4_deg 15.541 r_dihedral_angle_3_deg 14.677 r_dihedral_angle_1_deg 4.536 r_angle_other_deg 1.407 r_mcangle_it 1.301 r_angle_refined_deg 1.244 r_mcbond_it 0.735 r_mcbond_other 0.734 r_scbond_it 0.628 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 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 16432 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 8
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction