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The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VMA 2vma, 2vmb experimental model PDB 2VMB 2vma, 2vmb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1ul protein at 10mg/ml + 1ul reservoir: 12.5% PEG 400, 200mM CaOAc2, 100mM MES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.95 36.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.988 α = 90 b = 52.122 β = 90 c = 89.47 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 RIGAKU SATURN 944 multilayer (Varimax) 2006-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.7 45.05 95.6 0.06 0.06 15 3.78 23838 23838 17.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 79.1 0.223 0.223 3.3 1.97 1347
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 (All) 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 2vma, 2vmb 1.7 33.94 22632 22632 1223 95.96 0.15846 0.15846 0.15587 0.1655 0.20793 0.2118 RANDOM 9.193
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] 0.48 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.167 r_dihedral_angle_4_deg 15.622 r_dihedral_angle_3_deg 10.964 r_dihedral_angle_1_deg 3.925 r_scangle_it 3.178 r_scbond_it 1.998 r_angle_refined_deg 1.274 r_angle_other_deg 0.946 r_mcangle_it 0.919 r_mcbond_it 0.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.167 r_dihedral_angle_4_deg 15.622 r_dihedral_angle_3_deg 10.964 r_dihedral_angle_1_deg 3.925 r_scangle_it 3.178 r_scbond_it 1.998 r_angle_refined_deg 1.274 r_angle_other_deg 0.946 r_mcangle_it 0.919 r_mcbond_it 0.519 r_symmetry_vdw_other 0.27 r_nbd_refined 0.246 r_symmetry_hbond_refined 0.241 r_symmetry_vdw_refined 0.235 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.173 r_mcbond_other 0.163 r_metal_ion_refined 0.109 r_symmetry_metal_ion_refined 0.089 r_nbtor_other 0.082 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1808 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing