X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YC6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR
Crystal Properties
Matthews coefficientSolvent content
2.4750.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.995α = 90
b = 149.202β = 92.23
c = 87.26γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.7587.3599.80.098.83.845022
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)
12.7587.3599.50.81.43.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4YC62.7587.3542835218799.680.22920.226910.2737RANDOM73.119
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]
2.38-0.28-3.060.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.155
r_dihedral_angle_4_deg20.086
r_dihedral_angle_3_deg19.603
r_long_range_B_refined11.675
r_long_range_B_other11.675
r_scangle_other8.029
r_mcangle_other8.019
r_mcangle_it8.018
r_dihedral_angle_1_deg6.267
r_mcbond_it5.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.155
r_dihedral_angle_4_deg20.086
r_dihedral_angle_3_deg19.603
r_long_range_B_refined11.675
r_long_range_B_other11.675
r_scangle_other8.029
r_mcangle_other8.019
r_mcangle_it8.018
r_dihedral_angle_1_deg6.267
r_mcbond_it5.129
r_mcbond_other5.125
r_scbond_it4.995
r_scbond_other4.994
r_angle_other_deg3.653
r_angle_refined_deg1.54
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_other0.007
r_gen_planes_refined0.006
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 Atoms11742
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing