X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4U0T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5298ADC-7 (3mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/phosphate/glycine
Crystal Properties
Matthews coefficientSolvent content
2.1843.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.712α = 90
b = 81.651β = 112.84
c = 106.415γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002014-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.9598.07399.60.090.99711.94.1101377
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.9699.60.7060.7192.34.2

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 REPLACEMENTTHROUGHOUT4U0T1.9598.0796260499599.450.189980.187080.24619RANDOM35.77
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]
-0.260.99-21.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.597
r_dihedral_angle_3_deg15.61
r_dihedral_angle_4_deg13.168
r_dihedral_angle_1_deg7.074
r_long_range_B_refined6.23
r_long_range_B_other6.211
r_scangle_other4.942
r_mcangle_it3.954
r_mcangle_other3.954
r_scbond_it3.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.597
r_dihedral_angle_3_deg15.61
r_dihedral_angle_4_deg13.168
r_dihedral_angle_1_deg7.074
r_long_range_B_refined6.23
r_long_range_B_other6.211
r_scangle_other4.942
r_mcangle_it3.954
r_mcangle_other3.954
r_scbond_it3.381
r_scbond_other3.38
r_mcbond_it2.924
r_mcbond_other2.924
r_angle_refined_deg1.915
r_angle_other_deg1.109
r_chiral_restr0.147
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 Atoms11177
Nucleic Acid Atoms
Solvent Atoms628
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building