X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QUW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.12910.2M L-proline, 0.1M Hepes pH 7.1, 25%(w/v) PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3547.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.628α = 90
b = 61.984β = 90
c = 124.781γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.715099.85239152286
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.711.74100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4QUW1.7143.7034968749558266399.740.1890.1890.212RANDOM15.333
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]
-0.11-0.10.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.686
r_dihedral_angle_4_deg15.716
r_dihedral_angle_3_deg12.555
r_long_range_B_refined5.007
r_long_range_B_other4.512
r_dihedral_angle_1_deg3.965
r_angle_other_deg3.603
r_scangle_other2.43
r_scbond_it1.617
r_scbond_other1.616
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.686
r_dihedral_angle_4_deg15.716
r_dihedral_angle_3_deg12.555
r_long_range_B_refined5.007
r_long_range_B_other4.512
r_dihedral_angle_1_deg3.965
r_angle_other_deg3.603
r_scangle_other2.43
r_scbond_it1.617
r_scbond_other1.616
r_angle_refined_deg1.018
r_mcangle_it0.969
r_mcangle_other0.969
r_mcbond_it0.582
r_mcbond_other0.577
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_other0.004
r_gen_planes_refined0.003
r_bond_other_d
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 Atoms3560
Nucleic Acid Atoms
Solvent Atoms605
Heterogen Atoms22

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling