4UAV

Crystal structure of CbbY (AT3G48420) from Arabidobsis thaliana


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UARPDB entry 4UAR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529125 % (wt/vol) PEG-6000 and 0.1 M Tris-HCl pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.7254.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.725α = 90
b = 140.041β = 90
c = 87.107γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.000ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.370.02197.90.0490.0580.02913.23.77034770347
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3795.30.6240.6240.371.23.69877

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 REPLACEMENTTHROUGHOUTPDB entry 4UAR1.33070149353097.380.13810.13630.172RANDOM17.581
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]
-0.56-0.541.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.178
r_sphericity_free30.412
r_dihedral_angle_4_deg22.351
r_dihedral_angle_3_deg13.157
r_sphericity_bonded10.97
r_rigid_bond_restr6.645
r_dihedral_angle_1_deg5.544
r_angle_refined_deg2.086
r_angle_other_deg0.974
r_chiral_restr0.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.178
r_sphericity_free30.412
r_dihedral_angle_4_deg22.351
r_dihedral_angle_3_deg13.157
r_sphericity_bonded10.97
r_rigid_bond_restr6.645
r_dihedral_angle_1_deg5.544
r_angle_refined_deg2.086
r_angle_other_deg0.974
r_chiral_restr0.145
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1866
Nucleic Acid Atoms
Solvent Atoms377
Heterogen Atoms1

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction
XSCALEdata reduction