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% w/v PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.0439.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.52α = 104.83
b = 41.324β = 90.03
c = 76.36γ = 91.18
Symmetry
Space GroupP 1

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
11.6273.8287.30.0890.9945.83.951765
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)
11.621.6549.10.6520.5781.33.9

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 REPLACEMENTTHROUGHOUT2GDN1.6273.82491662394870.210660.209060.24393RANDOM14.727
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]
-0.91-0.02-0.271.18-0.26-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.124
r_dihedral_angle_4_deg19.228
r_dihedral_angle_3_deg13.221
r_dihedral_angle_1_deg6.623
r_long_range_B_refined3.703
r_long_range_B_other3.7
r_scangle_other2.665
r_mcangle_other2.178
r_mcangle_it2.177
r_angle_refined_deg1.858
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.124
r_dihedral_angle_4_deg19.228
r_dihedral_angle_3_deg13.221
r_dihedral_angle_1_deg6.623
r_long_range_B_refined3.703
r_long_range_B_other3.7
r_scangle_other2.665
r_mcangle_other2.178
r_mcangle_it2.177
r_angle_refined_deg1.858
r_scbond_it1.759
r_scbond_other1.758
r_mcbond_it1.426
r_mcbond_other1.421
r_angle_other_deg1.087
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms4017
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing