X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42740.1 M sodium acetate, pH 4, 2.6 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.346.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.58α = 90
b = 57.58β = 90
c = 183.71γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7254.9499.71127.916931
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.750.1081

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 REPLACEMENTTHROUGHOUTPDB entry 2QCB1.7254.941607283499.510.136010.134160.16788RANDOM21.139
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]
0.180.18-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.16
r_sphericity_free22.272
r_sphericity_bonded13.959
r_dihedral_angle_4_deg13.812
r_dihedral_angle_3_deg13.37
r_dihedral_angle_1_deg7.223
r_scangle_other6.163
r_long_range_B_refined5.824
r_long_range_B_other5.805
r_scbond_other5.702
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.16
r_sphericity_free22.272
r_sphericity_bonded13.959
r_dihedral_angle_4_deg13.812
r_dihedral_angle_3_deg13.37
r_dihedral_angle_1_deg7.223
r_scangle_other6.163
r_long_range_B_refined5.824
r_long_range_B_other5.805
r_scbond_other5.702
r_scbond_it5.701
r_rigid_bond_restr4.962
r_mcangle_other3.987
r_mcangle_it3.975
r_mcbond_it3.126
r_mcbond_other3.002
r_angle_refined_deg2.584
r_angle_other_deg1.139
r_chiral_restr0.153
r_bond_refined_d0.029
r_gen_planes_refined0.012
r_bond_other_d0.005
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 Atoms58
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing