X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZQ9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2 M zinc acetate, 0.1 M cacodylate buffer, 18% w/v polyethylene glycol 8000.
Crystal Properties
Matthews coefficientSolvent content
2.141.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 21.109α = 105.858
b = 26.722β = 97.598
c = 38.971γ = 90.857
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.283PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim 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
11.737880.10.1420.9865.11.915768
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.80.350.4960.8842.02

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-VALUE6ZQ91.737827142392.5060.1910.18840.247914.819
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]
-0.061.067-0.8131.12-0.653-0.398
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.593
r_lrange_other3.702
r_angle_other_deg2.424
r_angle_refined_deg1.638
r_scangle_it1.336
r_scangle_other1.335
r_scbond_other0.947
r_scbond_it0.946
r_xyhbond_nbd_refined0.286
r_symmetry_nbd_other0.269
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it4.593
r_lrange_other3.702
r_angle_other_deg2.424
r_angle_refined_deg1.638
r_scangle_it1.336
r_scangle_other1.335
r_scbond_other0.947
r_scbond_it0.946
r_xyhbond_nbd_refined0.286
r_symmetry_nbd_other0.269
r_nbtor_refined0.249
r_nbd_refined0.215
r_symmetry_xyhbond_nbd_refined0.207
r_nbd_other0.19
r_metal_ion_refined0.179
r_symmetry_nbd_refined0.148
r_symmetry_nbtor_other0.097
r_chiral_restr0.088
r_symmetry_xyhbond_nbd_other0.038
r_gen_planes_refined0.018
r_bond_refined_d0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms676
Solvent Atoms162
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing