1R8M

SEC7 DOMAIN OF THE ARF EXCHANGE FACTOR ARNO WITH BREFELDIN A-SENSITIZING MUTATIONS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PBVPDB ENTRY 1PBV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP828920% PEG 3350, 190mM Sodium Formate, 100mM Hepes, 18mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2445.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.429α = 90
b = 95.775β = 101.67
c = 33.665γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
21x-ray100 M
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979ESRFBM30A
2SYNCHROTRONESRF BEAMLINE ID14-30.933ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1,21.7330.066184.52108217.61
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)
1,21.71.7565.50.12251.76

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PBV1.732.972108219998108393.120.194140.192090.23136RANDOM15.946
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]
-0.190.59-0.591.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.332
r_scangle_it5.98
r_scbond_it3.821
r_mcangle_it2.245
r_angle_refined_deg1.942
r_mcbond_it1.306
r_angle_other_deg1.091
r_symmetry_vdw_refined0.365
r_symmetry_vdw_other0.328
r_nbd_other0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.332
r_scangle_it5.98
r_scbond_it3.821
r_mcangle_it2.245
r_angle_refined_deg1.942
r_mcbond_it1.306
r_angle_other_deg1.091
r_symmetry_vdw_refined0.365
r_symmetry_vdw_other0.328
r_nbd_other0.24
r_nbd_refined0.235
r_xyhbond_nbd_refined0.164
r_symmetry_hbond_refined0.163
r_chiral_restr0.11
r_nbtor_other0.093
r_bond_refined_d0.025
r_gen_planes_other0.023
r_gen_planes_refined0.017
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1593
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
AMoREphasing