X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U4X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92910.1 M BICINE pH 9.0, 2.0 M Magnesium chloride hexahydrate
Crystal Properties
Matthews coefficientSolvent content
3.6366.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.659α = 90
b = 86.659β = 90
c = 137.066γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97918APS24-ID-E

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
12.175099.60.06917.216.432051
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)
12.172.2199.20.9910.851213.2

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 REPLACEMENTTHROUGHOUT2.1745.7330483152199.460.201770.200640.22466RANDOM45.094
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]
0.290.140.29-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.775
r_dihedral_angle_3_deg15.016
r_dihedral_angle_4_deg14.759
r_long_range_B_other10.396
r_long_range_B_refined10.391
r_scangle_other8.749
r_dihedral_angle_1_deg7.807
r_scbond_it6.445
r_scbond_other6.443
r_mcangle_it6.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.775
r_dihedral_angle_3_deg15.016
r_dihedral_angle_4_deg14.759
r_long_range_B_other10.396
r_long_range_B_refined10.391
r_scangle_other8.749
r_dihedral_angle_1_deg7.807
r_scbond_it6.445
r_scbond_other6.443
r_mcangle_it6.118
r_mcangle_other6.116
r_mcbond_it4.801
r_mcbond_other4.771
r_angle_refined_deg2.006
r_angle_other_deg1.468
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.012
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 Atoms2574
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms48

Software

Software
Software NamePurpose
HKL-3000data scaling
PHASERphasing
REFMACrefinement