X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthernucleotide-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
2.2445.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.235α = 81.75
b = 58.296β = 86.83
c = 69.243γ = 73.79
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00000Photon FactoryAR-NW12A

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
12.0810096.90.0640.06411.32.2496311135.5
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)
12.082.1893.50.3232.41.9

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 REPLACEMENTTHROUGHOUTnucleotide-free Ara7/AtVps9a which was solved by MAD2.0868.5247099252995.770.229770.226950.28178RANDOM38.447
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]
-0.470.260.270.110.20.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.587
r_dihedral_angle_4_deg20.182
r_dihedral_angle_3_deg18.68
r_dihedral_angle_1_deg6.303
r_scangle_it2.855
r_scbond_it1.773
r_angle_refined_deg1.458
r_mcangle_it1.276
r_mcbond_it0.732
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.587
r_dihedral_angle_4_deg20.182
r_dihedral_angle_3_deg18.68
r_dihedral_angle_1_deg6.303
r_scangle_it2.855
r_scbond_it1.773
r_angle_refined_deg1.458
r_mcangle_it1.276
r_mcbond_it0.732
r_nbtor_refined0.301
r_symmetry_vdw_refined0.256
r_nbd_refined0.22
r_xyhbond_nbd_refined0.188
r_chiral_restr0.109
r_symmetry_hbond_refined0.094
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6480
Nucleic Acid Atoms
Solvent Atoms326
Heterogen Atoms56

Software

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