X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GDN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.1 M Tris-HCl, pH 7.0 1.7 M NH4H2PO4
Crystal Properties
Matthews coefficientSolvent content
4.3571.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.864α = 90
b = 108.864β = 90
c = 260.577γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4M2016-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9677ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.5449.7399.90.0340.99918.913.6714649
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.542.6399.90.490.7011.714.1

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 REPLACEMENTTHROUGHOUT2GDN2.5449.7349780262899.620.229450.2280.25634RANDOM63.052
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]
2.12.1-4.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.543
r_dihedral_angle_4_deg20.006
r_dihedral_angle_3_deg15.979
r_long_range_B_refined9.707
r_long_range_B_other9.706
r_scangle_other8.234
r_mcangle_it6.966
r_mcangle_other6.965
r_dihedral_angle_1_deg6.616
r_scbond_it6.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.543
r_dihedral_angle_4_deg20.006
r_dihedral_angle_3_deg15.979
r_long_range_B_refined9.707
r_long_range_B_other9.706
r_scangle_other8.234
r_mcangle_it6.966
r_mcangle_other6.965
r_dihedral_angle_1_deg6.616
r_scbond_it6.003
r_scbond_other6.002
r_mcbond_it5.161
r_mcbond_other5.145
r_angle_refined_deg1.757
r_angle_other_deg1.082
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms5885
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing