3OV5

Atomic structure of the Xanthomonas citri VirB7 globular domain.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherGlobular domain from NMR structure of the same protein.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529114 mg/mL protein in 5 mM Tris-Cl pH 7.5 and 25 mM sodium chloride was submitted to vapor diffusion sitting-drop crystallization trials at 291 K. Large plates appeared after one day over a reservoir solution comprising 1.4 M ammonium sulphate and 4 % (v/v) isopropyl alcohol. Reservoir solution supplemented with 25 % (v/v) glycerol was used as cryoprotectant. , VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
1.7831.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 27.76α = 90
b = 55.81β = 90
c = 83.097γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX20.9537LNLSW01B-MX2

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
11.043096.30.06834.812.130386303205.4
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)
11.041.08790.2935.18.92449

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 REPLACEMENTTHROUGHOUTGlobular domain from NMR structure of the same protein.1.0423.812879628796152496.320.13120.13120.130140.15161RANDOM10.366
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]
0.36-1.210.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.88
r_dihedral_angle_4_deg15.847
r_dihedral_angle_3_deg10.476
r_sphericity_free7.893
r_dihedral_angle_1_deg7.195
r_sphericity_bonded6.875
r_scangle_it3.281
r_scbond_it2.675
r_mcangle_it2.2
r_angle_refined_deg1.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.88
r_dihedral_angle_4_deg15.847
r_dihedral_angle_3_deg10.476
r_sphericity_free7.893
r_dihedral_angle_1_deg7.195
r_sphericity_bonded6.875
r_scangle_it3.281
r_scbond_it2.675
r_mcangle_it2.2
r_angle_refined_deg1.69
r_mcbond_it1.546
r_rigid_bond_restr1.341
r_nbtor_refined0.311
r_symmetry_vdw_refined0.271
r_nbd_refined0.224
r_symmetry_hbond_refined0.213
r_xyhbond_nbd_refined0.14
r_chiral_restr0.106
r_bond_refined_d0.013
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms619
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms4

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling