X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5281zinc sulfate, polyethylene glycol monomethyl ether 500 and 0.1 M sodium MES at pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.8568.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.92α = 90
b = 170.92β = 90
c = 111.061γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9792Australian SynchrotronMX2

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
11.6519.7699.90.0790.0230.99920.913.4114035
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)
11.651.711.3960.3840.6891.8

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-VALUE3wmt1.6519.76114035569899.8970.1530.15210.173830.724
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]
-0.272-0.136-0.2720.881
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.105
r_dihedral_angle_4_deg19.133
r_dihedral_angle_3_deg11.745
r_lrange_it6.792
r_lrange_other6.487
r_dihedral_angle_1_deg6.247
r_scangle_other5.593
r_scangle_it5.469
r_scbond_other3.9
r_scbond_it3.683
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.105
r_dihedral_angle_4_deg19.133
r_dihedral_angle_3_deg11.745
r_lrange_it6.792
r_lrange_other6.487
r_dihedral_angle_1_deg6.247
r_scangle_other5.593
r_scangle_it5.469
r_scbond_other3.9
r_scbond_it3.683
r_mcangle_it3.464
r_mcangle_other3.464
r_angle_other_deg3.165
r_mcbond_it2.562
r_mcbond_other2.562
r_angle_refined_deg1.88
r_xyhbond_nbd_refined0.232
r_nbd_refined0.219
r_symmetry_nbd_other0.214
r_symmetry_nbd_refined0.212
r_nbd_other0.187
r_nbtor_refined0.178
r_symmetry_xyhbond_nbd_refined0.146
r_metal_ion_refined0.123
r_symmetry_metal_ion_refined0.112
r_symmetry_nbtor_other0.104
r_chiral_restr0.096
r_bond_other_d0.035
r_gen_planes_other0.019
r_bond_refined_d0.014
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4280
Nucleic Acid Atoms
Solvent Atoms775
Heterogen Atoms337

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing