X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Y72 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor
Crystal Properties
Matthews coefficientSolvent content
2.4649.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.132α = 90
b = 53.782β = 98.26
c = 180.213γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.987DiamondI04

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
1289.171000.096.93.750412
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)
122.051001.011.13.7

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 REPLACEMENTTHROUGHOUT4Y72289.1747927248599.910.191960.189440.23918RANDOM47.989
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]
1.62-1.180.85-2.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.706
r_dihedral_angle_4_deg19.962
r_dihedral_angle_3_deg17.828
r_long_range_B_other9.533
r_long_range_B_refined9.523
r_scangle_other7.301
r_dihedral_angle_1_deg6.245
r_mcangle_it5.702
r_mcangle_other5.701
r_scbond_it4.892
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.706
r_dihedral_angle_4_deg19.962
r_dihedral_angle_3_deg17.828
r_long_range_B_other9.533
r_long_range_B_refined9.523
r_scangle_other7.301
r_dihedral_angle_1_deg6.245
r_mcangle_it5.702
r_mcangle_other5.701
r_scbond_it4.892
r_scbond_other4.891
r_mcbond_it3.997
r_mcbond_other3.997
r_angle_other_deg3.624
r_angle_refined_deg1.799
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.009
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 Atoms5143
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing