X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C41 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277.150.1 M Tris, 8% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.3647.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.02α = 90
b = 89.35β = 98.61
c = 144.7γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2009-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
1251.4398.640.0960.1130.0590.9979.43.68725532.45
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0393.150.8591.0190.5410.4851.33.36

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5C41251.4382880435598.610.198880.196770.23929RANDOM38.676
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]
-0.370.22-0.460.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.997
r_dihedral_angle_4_deg15.474
r_dihedral_angle_3_deg13.701
r_dihedral_angle_1_deg6.903
r_long_range_B_refined6.573
r_long_range_B_other6.462
r_scangle_other2.304
r_angle_refined_deg1.771
r_mcangle_it1.694
r_mcangle_other1.694
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.997
r_dihedral_angle_4_deg15.474
r_dihedral_angle_3_deg13.701
r_dihedral_angle_1_deg6.903
r_long_range_B_refined6.573
r_long_range_B_other6.462
r_scangle_other2.304
r_angle_refined_deg1.771
r_mcangle_it1.694
r_mcangle_other1.694
r_scbond_it1.535
r_scbond_other1.535
r_angle_other_deg1.438
r_mcbond_it1.096
r_mcbond_other1.095
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.003
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 Atoms9273
Nucleic Acid Atoms
Solvent Atoms978
Heterogen Atoms152

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing