X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AM9PDB ENTRY 3AM9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.429550mM potassium phosphate buffer (pH 6.5) containing 8.0 9.5% polyethylene glycol 4000, 30%(wt/vol) glycerol, 0.2mM EDTA, 5mM DTT, EVAPORATION, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6453.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.211α = 90
b = 124.53β = 91.07
c = 148.025γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1Photon FactoryAR-NW12A

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
12.0934.83177440177076

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3AM92.134.83168559888199.350.153470.150930.2018RANDOM25.134
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.017
r_dihedral_angle_4_deg17.076
r_dihedral_angle_3_deg15.291
r_dihedral_angle_1_deg6.582
r_scangle_it4.946
r_scbond_it3.179
r_angle_refined_deg2.025
r_mcangle_it1.87
r_mcbond_it1.073
r_chiral_restr0.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.017
r_dihedral_angle_4_deg17.076
r_dihedral_angle_3_deg15.291
r_dihedral_angle_1_deg6.582
r_scangle_it4.946
r_scbond_it3.179
r_angle_refined_deg2.025
r_mcangle_it1.87
r_mcbond_it1.073
r_chiral_restr0.143
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20037
Nucleic Acid Atoms
Solvent Atoms2029
Heterogen Atoms316

Software

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