4KAX

Crystal structure of the Grp1 PH domain in complex with Arf6-GTP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.829150 mM Tris, 20% PEG 4000, 0.2 M sodium citrate. Microseeding and TCEP were needed for large crystal growth, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.8556.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.595α = 90
b = 56.595β = 90
c = 274.371γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 3152010-12-03MSINGLE WAVELENGTH
2177
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.852098.94254541858-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8698.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8520-34289038245203998.930.201850.200120.23505RANDOM32.841
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]
0.380.38-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.827
r_dihedral_angle_4_deg17.029
r_dihedral_angle_3_deg11.847
r_dihedral_angle_1_deg5.394
r_scangle_it2.095
r_scbond_it1.239
r_angle_refined_deg1.142
r_mcangle_it0.981
r_mcbond_it0.519
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.827
r_dihedral_angle_4_deg17.029
r_dihedral_angle_3_deg11.847
r_dihedral_angle_1_deg5.394
r_scangle_it2.095
r_scbond_it1.239
r_angle_refined_deg1.142
r_mcangle_it0.981
r_mcbond_it0.519
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2501
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms99

Software

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