X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5L3Zligand a solvent free coordinate file was used

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.672770.1 M NaCacodylate pH6.67, 1M Na3-CITRATE
Crystal Properties
Matthews coefficientSolvent content
3.0559.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.313α = 90
b = 87.313β = 90
c = 174.382γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS EIGER X 16MMIRRORS2022-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.976254MAX IVBioMAX

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
12.429.0894.20.1730.0870.9926.94.12757039.5
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)
12.42.4993.80.7740.5230.72224.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.429.0826051144493.590.163530.161270.20344RANDOM41.083
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]
0.790.40.79-2.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.08
r_dihedral_angle_4_deg19.752
r_dihedral_angle_3_deg14.529
r_dihedral_angle_1_deg6.853
r_long_range_B_refined6.342
r_long_range_B_other6.287
r_scangle_other3.033
r_mcangle_it2.335
r_mcangle_other2.335
r_angle_refined_deg1.814
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.08
r_dihedral_angle_4_deg19.752
r_dihedral_angle_3_deg14.529
r_dihedral_angle_1_deg6.853
r_long_range_B_refined6.342
r_long_range_B_other6.287
r_scangle_other3.033
r_mcangle_it2.335
r_mcangle_other2.335
r_angle_refined_deg1.814
r_scbond_it1.789
r_scbond_other1.789
r_angle_other_deg1.382
r_mcbond_it1.339
r_mcbond_other1.338
r_chiral_restr0.076
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4182
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms252

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing