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 sodium acetate buffer, pH 5.0, 25% PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.1542.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.591α = 101.28
b = 41.683β = 90.11
c = 76.841γ = 90.43
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2016-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.9677ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.1975.3662.70.0630.0410.99811.33.296841
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.191.230.5730.4670.5231.22

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 REPLACEMENTTHROUGHOUT2GDN1.1975.3692053477362.690.167970.166830.18953RANDOM11.803
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]
-0.320.320.030.71-0.01-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.498
r_dihedral_angle_4_deg21.668
r_dihedral_angle_3_deg11.445
r_dihedral_angle_1_deg6.294
r_long_range_B_refined3.833
r_long_range_B_other3.833
r_scangle_other3.137
r_scbond_it2.234
r_scbond_other2.234
r_angle_refined_deg2.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.498
r_dihedral_angle_4_deg21.668
r_dihedral_angle_3_deg11.445
r_dihedral_angle_1_deg6.294
r_long_range_B_refined3.833
r_long_range_B_other3.833
r_scangle_other3.137
r_scbond_it2.234
r_scbond_other2.234
r_angle_refined_deg2.185
r_mcangle_other1.935
r_mcangle_it1.933
r_mcbond_it1.315
r_mcbond_other1.299
r_angle_other_deg1.124
r_chiral_restr0.153
r_bond_refined_d0.021
r_gen_planes_refined0.012
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 Atoms4045
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement