X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z64PDB entry 2Z64

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M Bicine, pH 7.5, 12% PEG10000
Crystal Properties
Matthews coefficientSolvent content
3.362.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.32α = 90
b = 128.32β = 90
c = 277.507γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-ID

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
12.95099.60.0838.77.951785
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.95

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 2Z642.9148.8149091263999.520.246350.243090.30775RANDOM100.275
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]
-4.03-4.038.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.272
r_dihedral_angle_3_deg19.301
r_dihedral_angle_4_deg18.119
r_long_range_B_refined9.959
r_long_range_B_other9.959
r_dihedral_angle_1_deg7.503
r_mcangle_it6.574
r_mcangle_other6.574
r_scangle_other6.448
r_mcbond_it4.026
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.272
r_dihedral_angle_3_deg19.301
r_dihedral_angle_4_deg18.119
r_long_range_B_refined9.959
r_long_range_B_other9.959
r_dihedral_angle_1_deg7.503
r_mcangle_it6.574
r_mcangle_other6.574
r_scangle_other6.448
r_mcbond_it4.026
r_mcbond_other4.026
r_scbond_it3.873
r_scbond_other3.872
r_angle_refined_deg1.68
r_angle_other_deg0.882
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms11873
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing