5FG3

Crystal structure of GDP-bound aIF5B from Aeropyrum pernix


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1 M Tris-HCl (pH7.5), 20%(w/v) PEG 3000, 0.2 M calcium acetate
Crystal Properties
Matthews coefficientSolvent content
2.5150.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.853α = 90
b = 97.448β = 94.77
c = 61.296γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102013-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
11.937.2195.40.06512.33.550764
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)
11.92.0288.10.3053.73

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 REPLACEMENTTHROUGHOUT1G7S1.937.2147238248693.480.196680.194240.24293RANDOM29.995
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]
0.1-0.03-0.140.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.53
r_dihedral_angle_4_deg15.148
r_dihedral_angle_3_deg15.139
r_dihedral_angle_1_deg6.343
r_long_range_B_refined5.08
r_long_range_B_other5.011
r_scangle_other3.459
r_mcangle_it2.538
r_mcangle_other2.538
r_scbond_other2.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.53
r_dihedral_angle_4_deg15.148
r_dihedral_angle_3_deg15.139
r_dihedral_angle_1_deg6.343
r_long_range_B_refined5.08
r_long_range_B_other5.011
r_scangle_other3.459
r_mcangle_it2.538
r_mcangle_other2.538
r_scbond_other2.118
r_scbond_it2.116
r_mcbond_it1.621
r_mcbond_other1.621
r_angle_refined_deg1.446
r_angle_other_deg0.924
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4692
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata collection
MOLREPphasing
XDSdata reduction
XSCALEdata scaling
Cootmodel building