X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q8F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291.150.1 M bicine pH 8.5, 20% (w/v) PEG 5000 monomethyl ether, 3% sucrose
Crystal Properties
Matthews coefficientSolvent content
2.4349.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.055α = 105.081
b = 94.665β = 89.959
c = 120.589γ = 93.826
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.578116.4298.50.1470.0890.9936.33.796699
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.5782.62398.21.4320.8550.3610.93.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.8116.41875517385798.5720.2110.20930.2508Random64.186
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]
-1.6290.695-0.2864.4011.406-3.193
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.533
r_dihedral_angle_6_deg14.982
r_lrange_other10.395
r_lrange_it10.394
r_dihedral_angle_1_deg7.451
r_dihedral_angle_2_deg6.625
r_scangle_it6.582
r_scangle_other6.581
r_mcangle_it6.08
r_mcangle_other6.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.533
r_dihedral_angle_6_deg14.982
r_lrange_other10.395
r_lrange_it10.394
r_dihedral_angle_1_deg7.451
r_dihedral_angle_2_deg6.625
r_scangle_it6.582
r_scangle_other6.581
r_mcangle_it6.08
r_mcangle_other6.08
r_scbond_it4.173
r_scbond_other4.173
r_mcbond_it3.926
r_mcbond_other3.926
r_angle_refined_deg1.205
r_angle_other_deg0.4
r_symmetry_xyhbond_nbd_refined0.331
r_symmetry_nbd_refined0.296
r_nbd_other0.259
r_nbd_refined0.21
r_xyhbond_nbd_refined0.201
r_symmetry_nbd_other0.187
r_nbtor_refined0.181
r_symmetry_xyhbond_nbd_other0.156
r_symmetry_nbtor_other0.077
r_chiral_restr0.057
r_ncsr_local_group_100.044
r_ncsr_local_group_190.043
r_ncsr_local_group_50.041
r_ncsr_local_group_140.041
r_ncsr_local_group_10.04
r_ncsr_local_group_90.04
r_ncsr_local_group_110.04
r_ncsr_local_group_150.04
r_ncsr_local_group_30.039
r_ncsr_local_group_200.039
r_ncsr_local_group_40.038
r_ncsr_local_group_80.038
r_ncsr_local_group_130.037
r_ncsr_local_group_160.037
r_ncsr_local_group_210.037
r_ncsr_local_group_220.037
r_ncsr_local_group_230.037
r_ncsr_local_group_240.036
r_ncsr_local_group_250.035
r_ncsr_local_group_70.034
r_ncsr_local_group_120.034
r_ncsr_local_group_270.034
r_ncsr_local_group_20.033
r_ncsr_local_group_260.033
r_ncsr_local_group_60.032
r_ncsr_local_group_180.032
r_ncsr_local_group_280.03
r_ncsr_local_group_170.026
r_metal_ion_refined0.007
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_chiral_restr_other0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21277
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing