X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ERK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.829336% PEG3350, 0.1 M Tris pH 8.8 10mg/mL protein.
Crystal Properties
Matthews coefficientSolvent content
2.9958.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.85α = 90
b = 77.15β = 90
c = 152.16γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Confocal mirrors2012-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

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
12.923.999.70.1076.66.711508
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.93.0699.50.3160.3420.1292.56.9

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 REPLACEMENTTHROUGHOUT2ERK2.923.891090854999.370.160390.156350.23907RANDOM48.336
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]
-0.391.63-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.268
r_dihedral_angle_4_deg17.744
r_dihedral_angle_3_deg17.497
r_long_range_B_refined8.445
r_long_range_B_other8.373
r_dihedral_angle_1_deg7.186
r_scangle_other6.537
r_mcangle_it5.744
r_mcangle_other5.744
r_scbond_it4.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.268
r_dihedral_angle_4_deg17.744
r_dihedral_angle_3_deg17.497
r_long_range_B_refined8.445
r_long_range_B_other8.373
r_dihedral_angle_1_deg7.186
r_scangle_other6.537
r_mcangle_it5.744
r_mcangle_other5.744
r_scbond_it4.47
r_scbond_other4.47
r_mcbond_it3.929
r_mcbond_other3.909
r_angle_refined_deg1.673
r_angle_other_deg1.218
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
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 Atoms2858
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing