X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XKU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.15200 mM ammonium phosphate dibasic 24 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4449.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.64α = 90
b = 110.7β = 106.97
c = 122.15γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.000Photon FactoryAR-NE3A

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
12.1735.1999.20.0840.9979.23.6101333
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)
12.172.2897.90.6440.6091.93.1

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 REPLACEMENTTHROUGHOUT1XKU2.1735.1996111519199.040.218370.21690.24526RANDOM44.762
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]
1.83-0.670.76-1.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.593
r_dihedral_angle_3_deg15.143
r_dihedral_angle_4_deg13.363
r_long_range_B_other9.384
r_long_range_B_refined9.379
r_scangle_other7.377
r_dihedral_angle_1_deg5.81
r_mcangle_it5.365
r_mcangle_other5.365
r_scbond_it4.767
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.593
r_dihedral_angle_3_deg15.143
r_dihedral_angle_4_deg13.363
r_long_range_B_other9.384
r_long_range_B_refined9.379
r_scangle_other7.377
r_dihedral_angle_1_deg5.81
r_mcangle_it5.365
r_mcangle_other5.365
r_scbond_it4.767
r_scbond_other4.76
r_mcbond_it3.708
r_mcbond_other3.706
r_angle_refined_deg1.736
r_angle_other_deg1.048
r_chiral_restr0.105
r_bond_refined_d0.015
r_gen_planes_refined0.008
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9985
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms192

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing