X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D2EPDB ENTRY 3D2E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION827715 % (w/v) polyethyleneglycol-6000, 100 mM Tris-HCl pH 8.0, 10 mM DTT, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.9758.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.5α = 90
b = 141.902β = 90
c = 151.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9780SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.3103.6951000.0730.0737.63.712439545.99
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)
12.32.421000.5060.5061.53.517980

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 DIFFRACTIONTHROUGHOUTPDB ENTRY 3D2E2.320124106624899.990.20.1970.244RANDOM44.114
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]
0.1-2.122.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.301
r_dihedral_angle_4_deg21.395
r_dihedral_angle_3_deg18.073
r_dihedral_angle_1_deg6.106
r_scangle_it2.596
r_scbond_it1.563
r_angle_refined_deg1.43
r_mcangle_it0.941
r_mcbond_it0.494
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.301
r_dihedral_angle_4_deg21.395
r_dihedral_angle_3_deg18.073
r_dihedral_angle_1_deg6.106
r_scangle_it2.596
r_scbond_it1.563
r_angle_refined_deg1.43
r_mcangle_it0.941
r_mcbond_it0.494
r_nbtor_refined0.297
r_symmetry_vdw_refined0.23
r_symmetry_hbond_refined0.211
r_nbd_refined0.198
r_xyhbond_nbd_refined0.14
r_chiral_restr0.103
r_bond_refined_d0.014
r_metal_ion_refined0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15391
Nucleic Acid Atoms
Solvent Atoms661
Heterogen Atoms76

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction