2VMA

The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
171UL PROTEIN, 1UL RESERVOIR: 12.5% PEG 400, 200MM CAOAC2, 100MM MES PH 7.0
Crystal Properties
Matthews coefficientSolvent content
238.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.816α = 90
b = 54.368β = 90
c = 88.587γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDMIRRORS2006-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.948.8296.60.0916.112.1118609
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9777.20.333.93.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTNONE1.946.321761594696.60.210.2080.255RANDOM17.5
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]
-0.071.74-1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.891
r_dihedral_angle_4_deg23.087
r_dihedral_angle_3_deg14.077
r_dihedral_angle_1_deg4.439
r_scangle_it3.003
r_scbond_it1.906
r_angle_refined_deg1.211
r_angle_other_deg0.969
r_mcangle_it0.953
r_mcbond_it0.639
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.891
r_dihedral_angle_4_deg23.087
r_dihedral_angle_3_deg14.077
r_dihedral_angle_1_deg4.439
r_scangle_it3.003
r_scbond_it1.906
r_angle_refined_deg1.211
r_angle_other_deg0.969
r_mcangle_it0.953
r_mcbond_it0.639
r_symmetry_vdw_other0.261
r_symmetry_hbond_refined0.254
r_symmetry_vdw_refined0.239
r_nbd_refined0.231
r_xyhbond_nbd_refined0.221
r_nbd_other0.186
r_nbtor_refined0.164
r_nbtor_other0.083
r_chiral_restr0.073
r_bond_refined_d0.012
r_bond_other_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1836
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms18

Software

Software
Software NamePurpose
ARP/wARPmodel building
CrystalCleardata scaling
SHELXphasing
SHARPphasing
DMphasing
ARP/wARPphasing
REFMACrefinement