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
2.141.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.71α = 105.1
b = 41.95β = 89.95
c = 76.93γ = 90.81
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9763ESRFID30B

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
11.940.585.96.821.973926
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.94

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 REPLACEMENTTHROUGHOUT2GDN1.940.530816162785.920.184430.182180.22679RANDOM12.06
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]
-0.140.060.110.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.204
r_dihedral_angle_4_deg18.686
r_dihedral_angle_3_deg13.659
r_dihedral_angle_1_deg6.776
r_long_range_B_refined4.247
r_long_range_B_other4.247
r_scangle_other2.428
r_angle_refined_deg1.877
r_mcangle_it1.855
r_mcangle_other1.855
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.204
r_dihedral_angle_4_deg18.686
r_dihedral_angle_3_deg13.659
r_dihedral_angle_1_deg6.776
r_long_range_B_refined4.247
r_long_range_B_other4.247
r_scangle_other2.428
r_angle_refined_deg1.877
r_mcangle_it1.855
r_mcangle_other1.855
r_scbond_it1.565
r_scbond_other1.565
r_mcbond_it1.194
r_mcbond_other1.157
r_angle_other_deg1.053
r_chiral_restr0.108
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 Atoms4013
Nucleic Acid Atoms
Solvent Atoms347
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing