X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BJ5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP728550mM phosphate buffer pH 6.5, 28-32% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.3748.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.06α = 74.8
b = 92.047β = 89.53
c = 94.664γ = 80.21
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98CCDADSC QUANTUM 3152008-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

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
12.1935.08920.07214.23.668079624972137
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2891.90.1130.11844963.45755

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 REPLACEMENTTHROUGHOUT1BJ52.19355906354279287191.340.232520.22940.2908RANDOM30.488
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]
-1.4-0.470.041.69-2.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.927
r_dihedral_angle_3_deg21.171
r_dihedral_angle_4_deg19.553
r_dihedral_angle_1_deg6.345
r_scangle_it4.158
r_scbond_it2.704
r_angle_refined_deg1.943
r_mcangle_it1.498
r_mcbond_it0.843
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.927
r_dihedral_angle_3_deg21.171
r_dihedral_angle_4_deg19.553
r_dihedral_angle_1_deg6.345
r_scangle_it4.158
r_scbond_it2.704
r_angle_refined_deg1.943
r_mcangle_it1.498
r_mcbond_it0.843
r_chiral_restr0.127
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms9160
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms256

Software

Software
Software NamePurpose
HKL-2000data collection
MLPHAREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling