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
2.7855.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.454α = 90
b = 99.075β = 105.18
c = 92.35γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2016-01-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
12.3589.131000.1390.99710.97.26560135.1
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)
12.352.411001.2111.76.9

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 SYNTHESISTHROUGHOUT5BYL2.3589.1362255331899.940.182440.180010.22783RANDOM49.218
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.872
r_dihedral_angle_4_deg16.933
r_dihedral_angle_3_deg15.169
r_long_range_B_refined7.691
r_long_range_B_other7.658
r_dihedral_angle_1_deg5.523
r_scangle_other3.801
r_angle_other_deg3.606
r_mcangle_it2.53
r_mcangle_other2.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.872
r_dihedral_angle_4_deg16.933
r_dihedral_angle_3_deg15.169
r_long_range_B_refined7.691
r_long_range_B_other7.658
r_dihedral_angle_1_deg5.523
r_scangle_other3.801
r_angle_other_deg3.606
r_mcangle_it2.53
r_mcangle_other2.53
r_scbond_it2.404
r_scbond_other2.404
r_mcbond_it1.638
r_mcbond_other1.637
r_angle_refined_deg1.537
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_other0.01
r_gen_planes_refined0.007
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 Atoms9817
Nucleic Acid Atoms
Solvent Atoms921
Heterogen Atoms129

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
REFMACphasing