X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H9G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2820.1 M Magnesium formate, 15% w/v Polyethylene glycol 3350, and 6% w/v 1,6-Hexanediol
Crystal Properties
Matthews coefficientSolvent content
1.7329.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.094α = 90
b = 76.059β = 90
c = 131.902γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDRAYONIX MX-3002018-01-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.078APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.765.9896.114.21459837
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.725

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 REPLACEMENTTHROUGHOUT3H9G1.765.9856811299196.090.156920.15470.19868RANDOM20.757
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]
0.90.57-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.475
r_dihedral_angle_4_deg21.547
r_dihedral_angle_3_deg15.16
r_dihedral_angle_1_deg6.75
r_long_range_B_refined5.216
r_long_range_B_other5.216
r_scangle_other4.339
r_scbond_it2.876
r_scbond_other2.875
r_mcangle_other2.584
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.475
r_dihedral_angle_4_deg21.547
r_dihedral_angle_3_deg15.16
r_dihedral_angle_1_deg6.75
r_long_range_B_refined5.216
r_long_range_B_other5.216
r_scangle_other4.339
r_scbond_it2.876
r_scbond_other2.875
r_mcangle_other2.584
r_mcangle_it2.582
r_mcbond_it1.748
r_mcbond_other1.747
r_angle_refined_deg1.7
r_angle_other_deg1.07
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.009
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 Atoms5564
Nucleic Acid Atoms
Solvent Atoms439
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHENIXmodel building
BUCCANEERmodel building
PHENIXphasing
XDSdata reduction