4NPS

Crystal Structure of Bep1 protein (VirB-translocated Bartonella effector protein) from Bartonella clarridgeiae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JK8PDB entry 2JK8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289Morpheus(g5): 10% PEG-20,000, 20% PEG MME 550, 0.1M MOPS/HEPES-Na, pH=7.5, 0.02M each Sodium Formate, Ammonium Acetate, Trisodium Citrate, Sodium Potassium L-Tartrate, Sodium Oxamate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.19α = 90
b = 97.85β = 90
c = 49.11γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium Lenses2013-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97857APS21-ID-F

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
11.958.6199.60.03627.795.12853528414-336.969
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)
11.91.9599.70.5223.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2JK81.958.612984928414143599.560.17370.17370.17170.2122RANDOM35.176
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]
1.43-0.81-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.214
r_dihedral_angle_4_deg18.947
r_dihedral_angle_3_deg13.463
r_dihedral_angle_1_deg6.329
r_mcangle_it1.983
r_angle_refined_deg1.502
r_mcbond_it1.408
r_mcbond_other1.377
r_angle_other_deg0.846
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.214
r_dihedral_angle_4_deg18.947
r_dihedral_angle_3_deg13.463
r_dihedral_angle_1_deg6.329
r_mcangle_it1.983
r_angle_refined_deg1.502
r_mcbond_it1.408
r_mcbond_other1.377
r_angle_other_deg0.846
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2163
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms8

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction