X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291100 mM PCTP 25% PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.6152.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.85α = 90
b = 123.3β = 96.9
c = 88.24γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2017-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.361.799.30.1170.1390.0730.96110.93.550253
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3897.20.2920.3460.1850.8993.43.4

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 REPLACEMENTTHROUGHOUT5YEE2.361.6547691256298.930.229930.227530.27448RANDOM32.106
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]
0.07-0.01-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.826
r_dihedral_angle_3_deg15.301
r_dihedral_angle_4_deg14.572
r_dihedral_angle_1_deg6.12
r_long_range_B_refined4.996
r_long_range_B_other4.945
r_angle_refined_deg1.484
r_angle_other_deg0.97
r_mcangle_it0.183
r_mcangle_other0.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.826
r_dihedral_angle_3_deg15.301
r_dihedral_angle_4_deg14.572
r_dihedral_angle_1_deg6.12
r_long_range_B_refined4.996
r_long_range_B_other4.945
r_angle_refined_deg1.484
r_angle_other_deg0.97
r_mcangle_it0.183
r_mcangle_other0.183
r_scangle_other0.12
r_mcbond_it0.099
r_mcbond_other0.099
r_chiral_restr0.081
r_scbond_it0.064
r_scbond_other0.064
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms7769
Nucleic Acid Atoms
Solvent Atoms478
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing