X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NSK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M Tris pH 6.8, 0.2 M MgCl2, 11 % (w/v) PEG 8000, 10 microM ZnCl2, 10 mM L-leucine
Crystal Properties
Matthews coefficientSolvent content
2.5451.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.368α = 90
b = 143.76β = 95.47
c = 270.085γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
12.432.7394.50.1175.73.3244412
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)
12.42.4488.70.35122.911362

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 REPLACEMENTTHROUGHOUT5NSK2.432.732321991198194.270.206890.205950.22508RANDOM34.619
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]
3.46-1.16-1.65-1.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.511
r_dihedral_angle_4_deg15.568
r_dihedral_angle_3_deg13.544
r_dihedral_angle_1_deg5.884
r_long_range_B_refined4.434
r_long_range_B_other4.407
r_scangle_other3.112
r_mcangle_it2.664
r_mcangle_other2.664
r_angle_other_deg2.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.511
r_dihedral_angle_4_deg15.568
r_dihedral_angle_3_deg13.544
r_dihedral_angle_1_deg5.884
r_long_range_B_refined4.434
r_long_range_B_other4.407
r_scangle_other3.112
r_mcangle_it2.664
r_mcangle_other2.664
r_angle_other_deg2.323
r_scbond_it1.938
r_scbond_other1.934
r_mcbond_it1.673
r_mcbond_other1.673
r_angle_refined_deg1.397
r_chiral_restr0.074
r_bond_refined_d0.014
r_bond_other_d0.008
r_gen_planes_refined0.008
r_gen_planes_other0.006
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 Atoms45554
Nucleic Acid Atoms
Solvent Atoms661
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing