X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27520% [w/v] PEG 3350, 0.2M sodium phosphate monobasic monohydrate
Crystal Properties
Matthews coefficientSolvent content
2.0238.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.019α = 90
b = 58.474β = 92.234
c = 138.13γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon 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
12.24699.90.0740.99916.36.8412432
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)
12.22.320.5590.847

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-VALUE3WMX2.24660750310099.8590.2110.20830.258247.019
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]
0.0040.0620.075-0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.584
r_dihedral_angle_4_deg20.163
r_dihedral_angle_3_deg16.304
r_lrange_other9.261
r_lrange_it9.254
r_dihedral_angle_1_deg6.91
r_scangle_it6.484
r_scangle_other6.484
r_mcangle_other6.408
r_mcangle_it6.407
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.584
r_dihedral_angle_4_deg20.163
r_dihedral_angle_3_deg16.304
r_lrange_other9.261
r_lrange_it9.254
r_dihedral_angle_1_deg6.91
r_scangle_it6.484
r_scangle_other6.484
r_mcangle_other6.408
r_mcangle_it6.407
r_mcbond_it4.507
r_mcbond_other4.503
r_scbond_it4.41
r_scbond_other4.409
r_angle_refined_deg1.476
r_angle_other_deg1.27
r_symmetry_xyhbond_nbd_refined0.351
r_nbd_other0.251
r_symmetry_xyhbond_nbd_other0.234
r_symmetry_nbd_refined0.208
r_nbd_refined0.202
r_xyhbond_nbd_refined0.199
r_symmetry_nbd_other0.181
r_nbtor_refined0.162
r_ncsr_local_group_60.107
r_ncsr_local_group_40.104
r_ncsr_local_group_30.102
r_ncsr_local_group_20.1
r_ncsr_local_group_10.098
r_ncsr_local_group_50.098
r_symmetry_nbtor_other0.078
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9335
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms176

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing