X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthernucloetide-free Ara7/AtVps9a which was solved by MAD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.528920% PEG3350, 200mM lithium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2445.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.466α = 81.9
b = 58.606β = 87.42
c = 68.974γ = 72.75
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.110093.20.0510.05112.51.9471211130.8
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)
12.12.1870.90.2771.91.5

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 REPLACEMENTTHROUGHOUTnucloetide-free Ara7/AtVps9a which was solved by MAD2.168.3644747237492.790.215990.213690.259RANDOM34.821
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]
-0.80.49-0.190.41-0.140.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.716
r_dihedral_angle_4_deg20.342
r_dihedral_angle_3_deg16.878
r_dihedral_angle_1_deg5.498
r_scangle_it2.561
r_scbond_it1.551
r_angle_refined_deg1.205
r_mcangle_it1.152
r_mcbond_it0.668
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.716
r_dihedral_angle_4_deg20.342
r_dihedral_angle_3_deg16.878
r_dihedral_angle_1_deg5.498
r_scangle_it2.561
r_scbond_it1.551
r_angle_refined_deg1.205
r_mcangle_it1.152
r_mcbond_it0.668
r_nbtor_refined0.299
r_symmetry_vdw_refined0.232
r_nbd_refined0.2
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.103
r_chiral_restr0.091
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6266
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing