X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WP9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.62930.1 M HEPES-NaOH pH 8.6, 0.95 M ammonium sulfate and 0.1 M lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.3864

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.427α = 90
b = 207.281β = 90
c = 100.784γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9800Photon FactoryBL-17A

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
11.947.6299.90.1070.0450.99712.96.714199015.45
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)
11.92.0199.60.4670.1970.8884.26.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3WP91.90447.62141916711999.8890.1370.13660.13510.1641Random selection19.482
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]
-0.4810.916-0.435
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.994
r_dihedral_angle_3_deg10.629
r_dihedral_angle_1_deg7.204
r_lrange_it6.661
r_lrange_other6.147
r_scangle_it4.535
r_scangle_other4.534
r_dihedral_angle_4_deg3.676
r_scbond_it3.075
r_scbond_other3.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.994
r_dihedral_angle_3_deg10.629
r_dihedral_angle_1_deg7.204
r_lrange_it6.661
r_lrange_other6.147
r_scangle_it4.535
r_scangle_other4.534
r_dihedral_angle_4_deg3.676
r_scbond_it3.075
r_scbond_other3.074
r_mcangle_it2.959
r_mcangle_other2.959
r_mcbond_it1.951
r_mcbond_other1.947
r_angle_refined_deg1.695
r_angle_other_deg1.538
r_symmetry_xyhbond_nbd_refined0.23
r_nbd_refined0.204
r_symmetry_nbd_other0.179
r_xyhbond_nbd_refined0.176
r_nbtor_refined0.159
r_symmetry_nbd_refined0.14
r_nbd_other0.099
r_symmetry_nbtor_other0.079
r_chiral_restr0.076
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8442
Nucleic Acid Atoms
Solvent Atoms1534
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing