X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XWXTruncated after residue 203

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2 M Zinc Acetate 0.1 M Sodium Cacodylate pH 6.5 18% w/v PEG 8K
Crystal Properties
Matthews coefficientSolvent content
2.0239.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.333α = 90
b = 89.374β = 90
c = 47.497γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2021-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.87313ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6247.54299.940.99810.836.878744
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.621.680.374

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.6247.54241528203499.9660.1780.17630.21325.413
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]
-1.8840.8811.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.756
r_dihedral_angle_3_deg14.295
r_lrange_other8.791
r_lrange_it8.784
r_dihedral_angle_1_deg8.297
r_scangle_it7.199
r_scangle_other7.198
r_dihedral_angle_2_deg6.085
r_scbond_it4.998
r_scbond_other4.997
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.756
r_dihedral_angle_3_deg14.295
r_lrange_other8.791
r_lrange_it8.784
r_dihedral_angle_1_deg8.297
r_scangle_it7.199
r_scangle_other7.198
r_dihedral_angle_2_deg6.085
r_scbond_it4.998
r_scbond_other4.997
r_mcangle_it4.32
r_mcangle_other4.319
r_mcbond_it3.409
r_mcbond_other3.326
r_angle_refined_deg1.341
r_angle_other_deg0.461
r_symmetry_nbd_refined0.354
r_nbd_other0.32
r_nbd_refined0.228
r_symmetry_nbd_other0.208
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.167
r_symmetry_xyhbond_nbd_refined0.149
r_metal_ion_refined0.126
r_symmetry_metal_ion_refined0.125
r_symmetry_nbtor_other0.084
r_chiral_restr0.071
r_symmetry_xyhbond_nbd_other0.061
r_gen_planes_refined0.016
r_bond_refined_d0.006
r_gen_planes_other0.004
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2798
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing