X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29520% [w/v] PEG 3350, 0.2M magnesium acetate
Crystal Properties
Matthews coefficientSolvent content
3.7567.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.108α = 90
b = 180.932β = 90.007
c = 141.713γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-03-05MSINGLE 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
12.149.41000.087115.57878278
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)
12.12.220.570.895

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-VALUE3WMX2.10249.4125517630299.9630.2090.20720.234831.893
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]
2.3620.103-0.899-1.463
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.557
r_dihedral_angle_4_deg19.767
r_dihedral_angle_3_deg14.502
r_dihedral_angle_1_deg7.012
r_lrange_other6.828
r_lrange_it6.824
r_scangle_it5.096
r_scangle_other5.096
r_mcangle_it3.966
r_mcangle_other3.966
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.557
r_dihedral_angle_4_deg19.767
r_dihedral_angle_3_deg14.502
r_dihedral_angle_1_deg7.012
r_lrange_other6.828
r_lrange_it6.824
r_scangle_it5.096
r_scangle_other5.096
r_mcangle_it3.966
r_mcangle_other3.966
r_scbond_other3.492
r_scbond_it3.491
r_mcbond_it2.959
r_mcbond_other2.959
r_angle_refined_deg1.607
r_angle_other_deg1.406
r_symmetry_nbd_refined0.541
r_nbd_other0.439
r_nbd_refined0.213
r_symmetry_xyhbond_nbd_refined0.186
r_symmetry_nbd_other0.183
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.166
r_symmetry_xyhbond_nbd_other0.104
r_symmetry_nbtor_other0.081
r_ncsr_local_group_60.081
r_ncsr_local_group_40.079
r_chiral_restr0.078
r_ncsr_local_group_30.075
r_ncsr_local_group_10.074
r_xyhbond_nbd_other0.063
r_ncsr_local_group_50.059
r_ncsr_local_group_20.052
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9460
Nucleic Acid Atoms
Solvent Atoms574
Heterogen Atoms256

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing