X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5X0B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9293PEG 3350, serine
Crystal Properties
Matthews coefficientSolvent content
2.1943.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.936α = 90
b = 69.602β = 90
c = 87.431γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2016-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.000SPring-8BL38B1

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
11.65509920.9729948

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5X0B1.655028412150499.80.233730.232470.257RANDOM28.517
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]
-0.57-0.491.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.232
r_dihedral_angle_3_deg12.2
r_dihedral_angle_4_deg9.741
r_dihedral_angle_1_deg7.263
r_long_range_B_refined4.123
r_long_range_B_other4.06
r_angle_refined_deg1.59
r_angle_other_deg0.941
r_scangle_other0.737
r_mcangle_it0.644
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.232
r_dihedral_angle_3_deg12.2
r_dihedral_angle_4_deg9.741
r_dihedral_angle_1_deg7.263
r_long_range_B_refined4.123
r_long_range_B_other4.06
r_angle_refined_deg1.59
r_angle_other_deg0.941
r_scangle_other0.737
r_mcangle_it0.644
r_mcangle_other0.643
r_scbond_it0.459
r_scbond_other0.459
r_mcbond_it0.368
r_mcbond_other0.368
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.003
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 Atoms1793
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
REFMACphasing