X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WMS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.528525% (w/v) PEG3350, 0.11M Mg formate
Crystal Properties
Matthews coefficientSolvent content
2.2545.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.373α = 90
b = 136.825β = 90
c = 38.549γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9998SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.780.499.10.0530.0570.020.99917.37.958681
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7390.30.8760.9720.4090.731.35.2

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 REPLACEMENTTHROUGHOUT1.780.455605307599.070.184440.182680.21557RANDOM36.35
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]
0.08-0.640.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.09
r_dihedral_angle_4_deg16.544
r_dihedral_angle_3_deg12.169
r_long_range_B_refined5.851
r_long_range_B_other5.67
r_dihedral_angle_1_deg4.995
r_angle_other_deg1.78
r_scangle_other1.424
r_angle_refined_deg1.216
r_mcangle_it1.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.09
r_dihedral_angle_4_deg16.544
r_dihedral_angle_3_deg12.169
r_long_range_B_refined5.851
r_long_range_B_other5.67
r_dihedral_angle_1_deg4.995
r_angle_other_deg1.78
r_scangle_other1.424
r_angle_refined_deg1.216
r_mcangle_it1.038
r_mcangle_other1.038
r_scbond_it0.868
r_scbond_other0.867
r_mcbond_it0.639
r_mcbond_other0.627
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms4021
Nucleic Acid Atoms
Solvent Atoms435
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
PHASERphasing
Aimlessdata scaling