X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5294.15Morpheus screen condition G8
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.046α = 78.76
b = 110.17β = 82.28
c = 118.516γ = 60.43
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-02-03MSINGLE 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)Rpim I (All)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
11.3895.4295.70.0770.0770.9977.32.99322508.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.381.4293.20.8010.8010.4771.32.8

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5aqd1.3895.428781704644494.70.1580.1550.211RANDOM15.91
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]
-0.150.080.27-0.18-0.360.41
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.746
r_dihedral_angle_2_deg35.364
r_dihedral_angle_4_deg16.138
r_dihedral_angle_3_deg12.717
r_sphericity_bonded10.923
r_long_range_B_refined5.757
r_dihedral_angle_1_deg5.119
r_long_range_B_other3.615
r_rigid_bond_restr3.107
r_scangle_other2.655
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.746
r_dihedral_angle_2_deg35.364
r_dihedral_angle_4_deg16.138
r_dihedral_angle_3_deg12.717
r_sphericity_bonded10.923
r_long_range_B_refined5.757
r_dihedral_angle_1_deg5.119
r_long_range_B_other3.615
r_rigid_bond_restr3.107
r_scangle_other2.655
r_angle_refined_deg2.596
r_scbond_it2.221
r_scbond_other2.216
r_mcangle_it1.977
r_mcangle_other1.977
r_mcbond_it1.621
r_mcbond_other1.621
r_angle_other_deg1.284
r_chiral_restr0.112
r_bond_refined_d0.018
r_gen_planes_other0.017
r_gen_planes_refined0.012
r_bond_other_d0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms31032
Nucleic Acid Atoms
Solvent Atoms7799
Heterogen Atoms2762

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing