X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529680-120mM MgCl2, 8% glycerol, 10% PEG 3350, 100mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8756.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.22α = 90
b = 99.67β = 104.9
c = 93.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal2013-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.190.2699.70.0950.1270.99584.19294037.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1495.21.18713.2

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 SYNTHESISTHROUGHOUT5BYL2.290.2677029407899.910.164340.162340.20214RANDOM46.315
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]
-0.42-0.581.05-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.266
r_dihedral_angle_3_deg13.859
r_dihedral_angle_4_deg13.082
r_long_range_B_refined9.41
r_long_range_B_other9.387
r_dihedral_angle_1_deg5.844
r_scangle_other4.531
r_mcangle_it3.024
r_mcangle_other3.024
r_scbond_it2.849
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.266
r_dihedral_angle_3_deg13.859
r_dihedral_angle_4_deg13.082
r_long_range_B_refined9.41
r_long_range_B_other9.387
r_dihedral_angle_1_deg5.844
r_scangle_other4.531
r_mcangle_it3.024
r_mcangle_other3.024
r_scbond_it2.849
r_scbond_other2.848
r_mcbond_it1.976
r_mcbond_other1.975
r_angle_refined_deg1.639
r_angle_other_deg1.358
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.009
r_gen_planes_other0.007
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 Atoms9726
Nucleic Acid Atoms
Solvent Atoms1098
Heterogen Atoms263

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
Cootmodel building