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
2.8156.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.169α = 90
b = 99.74β = 105.1
c = 92.97γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2016-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.1589.7699.80.0820.9968.43.48642434.2
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)
12.152.1997.20.6231.63

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 SYNTHESISTHROUGHOUT5BYL2.1589.7681863432899.70.169570.167390.2108RANDOM46.623
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_deg36.017
r_dihedral_angle_4_deg14.697
r_dihedral_angle_3_deg13.945
r_long_range_B_refined9.631
r_long_range_B_other9.607
r_dihedral_angle_1_deg5.612
r_scangle_other4.416
r_angle_other_deg3.554
r_mcangle_it2.842
r_mcangle_other2.842
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.017
r_dihedral_angle_4_deg14.697
r_dihedral_angle_3_deg13.945
r_long_range_B_refined9.631
r_long_range_B_other9.607
r_dihedral_angle_1_deg5.612
r_scangle_other4.416
r_angle_other_deg3.554
r_mcangle_it2.842
r_mcangle_other2.842
r_scbond_it2.815
r_scbond_other2.814
r_mcbond_it1.856
r_mcbond_other1.855
r_angle_refined_deg1.631
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_other0.014
r_gen_planes_refined0.008
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 Atoms9712
Nucleic Acid Atoms
Solvent Atoms1323
Heterogen Atoms139

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building