X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.2 M NaBr; 0.1 M Bis Tris propane pH 8.5; 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2445.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.669α = 90
b = 79.444β = 90
c = 87.523γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.00ESRFID23-1

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
11.458.8299.980.0280.99911.421.910430116.12
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)
11.41.451000.330.8121.881.9

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 REPLACEMENTTHROUGHOUT4GNU1.458.8299250505199.970.167330.165230.2085RANDOM20.522
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]
-0.120.19-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.411
r_dihedral_angle_4_deg19.004
r_dihedral_angle_3_deg13.491
r_dihedral_angle_1_deg6.106
r_rigid_bond_restr5.527
r_scbond_it4.23
r_long_range_B_refined3.995
r_mcangle_it2.81
r_mcbond_it2.461
r_angle_refined_deg2.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.411
r_dihedral_angle_4_deg19.004
r_dihedral_angle_3_deg13.491
r_dihedral_angle_1_deg6.106
r_rigid_bond_restr5.527
r_scbond_it4.23
r_long_range_B_refined3.995
r_mcangle_it2.81
r_mcbond_it2.461
r_angle_refined_deg2.126
r_chiral_restr0.136
r_bond_refined_d0.016
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4080
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing