X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.2 M NH4NO3 20% w/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.0339.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.6α = 90
b = 76.41β = 90.7
c = 79.32γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.07ESRFID29

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
11.6379.3199.80.050.9979.76.658936
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)
11.631.6698.90.3770.7626.7

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 REPLACEMENTTHROUGHOUT2GDN1.6379.3156014292299.790.236010.234070.27514RANDOM16.679
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]
-1.650.430.291.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.014
r_dihedral_angle_4_deg19.881
r_dihedral_angle_3_deg13.113
r_dihedral_angle_1_deg6.544
r_long_range_B_refined3.435
r_long_range_B_other3.435
r_scangle_other2.69
r_mcangle_it2.122
r_mcangle_other2.122
r_angle_refined_deg1.895
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.014
r_dihedral_angle_4_deg19.881
r_dihedral_angle_3_deg13.113
r_dihedral_angle_1_deg6.544
r_long_range_B_refined3.435
r_long_range_B_other3.435
r_scangle_other2.69
r_mcangle_it2.122
r_mcangle_other2.122
r_angle_refined_deg1.895
r_scbond_it1.885
r_scbond_other1.885
r_mcbond_it1.501
r_mcbond_other1.501
r_angle_other_deg1.085
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.01
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 Atoms4036
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing