X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42742.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4
Crystal Properties
Matthews coefficientSolvent content
2.9257.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.72α = 90
b = 57.72β = 90
c = 183.46γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0000ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.745.966.90.09219.75.111863
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)
11.71.7364.31.9970.74.3

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 REPLACEMENTTHROUGHOUT2QCB1.745.91123358967.140.174880.171820.23397RANDOM23.625
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]
-0.25-0.250.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.324
r_dihedral_angle_4_deg19.268
r_dihedral_angle_3_deg13.143
r_sphericity_free12.044
r_sphericity_bonded10.914
r_dihedral_angle_1_deg7.62
r_scangle_other6.288
r_long_range_B_other6.087
r_long_range_B_refined6.064
r_scbond_it4.944
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.324
r_dihedral_angle_4_deg19.268
r_dihedral_angle_3_deg13.143
r_sphericity_free12.044
r_sphericity_bonded10.914
r_dihedral_angle_1_deg7.62
r_scangle_other6.288
r_long_range_B_other6.087
r_long_range_B_refined6.064
r_scbond_it4.944
r_scbond_other4.916
r_mcangle_other4.336
r_rigid_bond_restr4.328
r_mcangle_it4.308
r_mcbond_it3.767
r_mcbond_other3.593
r_angle_refined_deg2.523
r_angle_other_deg1.062
r_chiral_restr0.125
r_bond_refined_d0.025
r_gen_planes_refined0.01
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms924
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing