X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FOF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28820% PEG 3350, 0.2 M Sodium formate, 0.1 M Tris-HCl pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.8256.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.323α = 90
b = 102.627β = 90
c = 126.421γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2022-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)1.0000PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.8633.8997.170.0760.080.0250.99917.069.451961
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.930.479

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1FOF1.8633.8949328263397.180.178370.176090.22052RANDOM25.116
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.544
r_dihedral_angle_2_deg7.675
r_long_range_B_refined7.669
r_long_range_B_other7.276
r_dihedral_angle_1_deg6.494
r_scangle_other4.991
r_mcangle_it3.646
r_mcangle_other3.645
r_scbond_it3.196
r_scbond_other3.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.544
r_dihedral_angle_2_deg7.675
r_long_range_B_refined7.669
r_long_range_B_other7.276
r_dihedral_angle_1_deg6.494
r_scangle_other4.991
r_mcangle_it3.646
r_mcangle_other3.645
r_scbond_it3.196
r_scbond_other3.195
r_mcbond_it2.46
r_mcbond_other2.46
r_angle_refined_deg1.455
r_angle_other_deg0.53
r_chiral_restr0.08
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms3916
Nucleic Acid Atoms
Solvent Atoms519
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000phasing
PDB_EXTRACTdata extraction