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Type IV secretion system effector protein BepA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VY3 PDB ENTRY 2VY3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.25 30 MG/ML PROTEIN IN 20 MM TRIS_HCL (PH 8.0), 500 MM NACL AND 2 MM BETA-MERCAPTOETHANOL MIXED WITH 1.5 M AMMONIUM SULFATE, 10 MM TRIS-HCL (PH 8.25) AND 0.1 M LITHIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.86 56.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 229.902 α = 90 b = 229.902 β = 90 c = 308.994 γ = 120
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 MARRESEARCH 2007-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.95 83.62 92.6 0.11 5.34 2.91 55048
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 3.05 3.21 75.4 0.45 1.61 1.84
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 2VY3 3.05 30 52197 2796 92.1 0.246 0.244 0.2481 0.277 0.283 RANDOM 60.65
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] 0.27 0.13 0.27 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.771 r_dihedral_angle_3_deg 15.492 r_dihedral_angle_4_deg 12.73 r_dihedral_angle_1_deg 5.198 r_angle_refined_deg 1.017 r_angle_other_deg 0.821 r_scangle_it 0.709 r_scbond_it 0.448 r_mcangle_it 0.277 r_symmetry_vdw_other 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.771 r_dihedral_angle_3_deg 15.492 r_dihedral_angle_4_deg 12.73 r_dihedral_angle_1_deg 5.198 r_angle_refined_deg 1.017 r_angle_other_deg 0.821 r_scangle_it 0.709 r_scbond_it 0.448 r_mcangle_it 0.277 r_symmetry_vdw_other 0.235 r_symmetry_vdw_refined 0.232 r_mcbond_it 0.228 r_nbd_refined 0.223 r_nbtor_refined 0.18 r_nbd_other 0.167 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.142 r_nbtor_other 0.087 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 19008 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing