X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.92951.0 M malate, pH 8.0, Tris, 0.3 M NaCl, 1% n-nonyl-beta-D maltoside
Crystal Properties
Matthews coefficientSolvent content
2.3146.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.031α = 90
b = 96.284β = 90
c = 151.591γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

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
12.497596.90.113.82.613474
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)
12.492.5412.40.431.31.3

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 REPLACEMENTTHROUGHOUT1EMB2.49101246864475.710.179930.1750.27598RANDOM38.05
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]
-2.153.29-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.271
r_dihedral_angle_3_deg18.498
r_dihedral_angle_4_deg11.813
r_dihedral_angle_1_deg8.651
r_long_range_B_other6.697
r_long_range_B_refined6.696
r_scangle_other4.027
r_mcangle_it3.773
r_mcangle_other3.772
r_scbond_it2.547
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.271
r_dihedral_angle_3_deg18.498
r_dihedral_angle_4_deg11.813
r_dihedral_angle_1_deg8.651
r_long_range_B_other6.697
r_long_range_B_refined6.696
r_scangle_other4.027
r_mcangle_it3.773
r_mcangle_other3.772
r_scbond_it2.547
r_scbond_other2.546
r_mcbond_it2.381
r_mcbond_other2.378
r_angle_refined_deg1.853
r_angle_other_deg1.003
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3586
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing