X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B4E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5290Protein buffer was 10 mM Tris-HCl pH 8.0. Protein concentration 5 mg/ml. It was crystallised in the presence of 1 mM levulinic acid with 0.1 M HEPES pH 7.5, 10 % isopropanol and 20 % polyethylene glycol (PEG) 4000 in the well solution.
Crystal Properties
Matthews coefficientSolvent content
2.6854

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 205.561α = 90
b = 205.561β = 90
c = 199.171γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I021.04DiamondI02

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
13.47178.021000.11814.79.86335275.9
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)
13.473.61000.5484.89.9

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 REPLACEMENTTHROUGHOUT1b4e3.47178.0260159315499.990.15280.147620.25002RANDOM92.638
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]
-1.02-0.51-1.023.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.622
r_dihedral_angle_3_deg20.877
r_dihedral_angle_4_deg20.078
r_dihedral_angle_1_deg9.463
r_long_range_B_refined7.735
r_long_range_B_other7.735
r_mcangle_it5.045
r_mcangle_other5.045
r_scangle_other4.502
r_mcbond_it2.966
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.622
r_dihedral_angle_3_deg20.877
r_dihedral_angle_4_deg20.078
r_dihedral_angle_1_deg9.463
r_long_range_B_refined7.735
r_long_range_B_other7.735
r_mcangle_it5.045
r_mcangle_other5.045
r_scangle_other4.502
r_mcbond_it2.966
r_mcbond_other2.966
r_scbond_it2.571
r_scbond_other2.571
r_angle_refined_deg1.884
r_angle_other_deg1.161
r_chiral_restr0.11
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms31680
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
MOLREPphasing