X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IVI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.52952.2 M ammonium sulfate and 0.1 M Tris-HCl (pH 8.5), microbatch, temperature 295KK
Crystal Properties
Matthews coefficientSolvent content
5.0675.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.102α = 90
b = 149.102β = 90
c = 172.571γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702009-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A0.98000Photon FactoryAR-NE3A

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
11.85089398

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 REPLACEMENTTHROUGHOUT4IVI1.845.0384680447199.580.162430.161390.18216RANDOM28.221
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]
-1.18-1.182.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.294
r_sphericity_free27.141
r_dihedral_angle_4_deg13.039
r_dihedral_angle_3_deg12.004
r_sphericity_bonded8.95
r_dihedral_angle_1_deg5.566
r_rigid_bond_restr1.564
r_angle_refined_deg1.139
r_angle_other_deg0.749
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.294
r_sphericity_free27.141
r_dihedral_angle_4_deg13.039
r_dihedral_angle_3_deg12.004
r_sphericity_bonded8.95
r_dihedral_angle_1_deg5.566
r_rigid_bond_restr1.564
r_angle_refined_deg1.139
r_angle_other_deg0.749
r_chiral_restr0.069
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3086
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms42

Software

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