X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DJR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52930.1 M sodium acetate, 20 % w/v PEG 6000, 0.2 M lithium chloride
Crystal Properties
Matthews coefficientSolvent content
1.9537.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.079α = 90
b = 65.587β = 108.64
c = 96.266γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 2M2015-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8729ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.4568.7399.80.1256.44.4160263
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.471.151

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 REPLACEMENTTHROUGHOUT1DJR1.4568.73152246797399.450.176530.175240.20087RANDOM18.482
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]
0.14-0.04-0.140.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.517
r_dihedral_angle_4_deg25.905
r_dihedral_angle_1_deg15.187
r_dihedral_angle_3_deg14.407
r_long_range_B_other10.599
r_long_range_B_refined10.594
r_scangle_other10.423
r_scbond_it9.34
r_scbond_other9.339
r_mcangle_it5.262
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.517
r_dihedral_angle_4_deg25.905
r_dihedral_angle_1_deg15.187
r_dihedral_angle_3_deg14.407
r_long_range_B_other10.599
r_long_range_B_refined10.594
r_scangle_other10.423
r_scbond_it9.34
r_scbond_other9.339
r_mcangle_it5.262
r_mcangle_other5.262
r_mcbond_it4.543
r_mcbond_other4.543
r_angle_refined_deg1.682
r_angle_other_deg1.393
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms8130
Nucleic Acid Atoms
Solvent Atoms645
Heterogen Atoms173

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building