4XZJ

Crystal structure of ADP-ribosyltransferase Vis in complex with NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Y1W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729830% Jeffamine ED-2001, 0.1 M Hepes
Crystal Properties
Matthews coefficientSolvent content
2.6152.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.7α = 90
b = 52β = 90
c = 100.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2011-08-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
11.82094.70.044525.846.2523562
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)
11.81.991.80.17998.675.24

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4Y1W1.818.6323524119194.810.17670.17510.2054RANDOM23.386
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]
-0.471-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.06
r_dihedral_angle_4_deg14.998
r_dihedral_angle_3_deg12.927
r_dihedral_angle_1_deg5.832
r_angle_refined_deg1.424
r_angle_other_deg0.768
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.06
r_dihedral_angle_4_deg14.998
r_dihedral_angle_3_deg12.927
r_dihedral_angle_1_deg5.832
r_angle_refined_deg1.424
r_angle_other_deg0.768
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1756
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms44

Software

Software
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
SHELXphasing
PHASERphasing
XPREPdata reduction