1S9D

ARF1[DELTA 1-17]-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 DOMAIN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RRGPDB ENTRY 1RRG and coordinates of arf1[D1-17]/Gea2-Sec7 (Goldberg, J., (1998) Cell 95(2): 237-48)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP828929% PEG 3350, 40MM NH4CL, 40MM POTASSIUM FORMATE, 100MM TRIS, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.7355

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.462α = 90
b = 111.462β = 90
c = 74.534γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2003-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.980ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.83098.10.0526.212438144381422.76
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8597.10.4056.412.13319

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1RRG and coordinates of arf1[D1-17]/Gea2-Sec7 (Goldberg, J., (1998) Cell 95(2): 237-48)1.829.884381441588222599.540.1840.183970.181930.22148RANDOM19.91
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]
-1.95-1.953.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.862
r_scangle_it5.065
r_scbond_it3.243
r_mcangle_it2.081
r_angle_refined_deg1.94
r_mcbond_it1.233
r_angle_other_deg0.999
r_symmetry_vdw_other0.284
r_nbd_other0.256
r_symmetry_vdw_refined0.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.862
r_scangle_it5.065
r_scbond_it3.243
r_mcangle_it2.081
r_angle_refined_deg1.94
r_mcbond_it1.233
r_angle_other_deg0.999
r_symmetry_vdw_other0.284
r_nbd_other0.256
r_symmetry_vdw_refined0.249
r_nbd_refined0.226
r_xyhbond_nbd_refined0.176
r_symmetry_hbond_refined0.148
r_chiral_restr0.128
r_nbtor_other0.09
r_bond_refined_d0.025
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2830
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
CCP4phasing