X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CAQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.075 M succinic acid, pH7.0, 11% PEG 3350, and 25% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.3246.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.048α = 90
b = 99.221β = 90
c = 193.876γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7248.51000.052142.622.3202517
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.751.840.672

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7CAQ1.7248.062202517999899.640.1970.19630.212932.316
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]
0.01-0.0240.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.758
r_dihedral_angle_4_deg18.884
r_dihedral_angle_3_deg13.63
r_dihedral_angle_1_deg6.184
r_lrange_it5.017
r_lrange_other4.988
r_scangle_it3.095
r_scangle_other3.095
r_mcangle_it2.569
r_mcangle_other2.569
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.758
r_dihedral_angle_4_deg18.884
r_dihedral_angle_3_deg13.63
r_dihedral_angle_1_deg6.184
r_lrange_it5.017
r_lrange_other4.988
r_scangle_it3.095
r_scangle_other3.095
r_mcangle_it2.569
r_mcangle_other2.569
r_scbond_it1.976
r_scbond_other1.976
r_mcbond_it1.712
r_mcbond_other1.712
r_angle_other_deg1.297
r_angle_refined_deg1.252
r_nbd_refined0.192
r_symmetry_nbd_other0.173
r_nbtor_refined0.163
r_symmetry_xyhbond_nbd_refined0.142
r_nbd_other0.137
r_xyhbond_nbd_refined0.126
r_symmetry_nbd_refined0.095
r_symmetry_nbtor_other0.074
r_chiral_restr0.058
r_symmetry_xyhbond_nbd_other0.022
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13859
Nucleic Acid Atoms
Solvent Atoms781
Heterogen Atoms556

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing