X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LE7PDB ENTRY 4LE7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320% PEG 550 MME, 20% PEG 20K, 0.03 M CaCl2, 0.03 M MgCl2 0.1 M MOPS/HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.99α = 90
b = 160.65β = 90
c = 150.57γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9788DiamondI04

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
12.3754.9399.10.059194.4262422243.618
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)
12.372.4399.50.832.14.51922

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4LE72.3754.9322621524888132798.80.211280.211280.208870.25685RANDOM54.163
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]
-2.082.35-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.384
r_dihedral_angle_4_deg22.155
r_dihedral_angle_3_deg16.224
r_dihedral_angle_1_deg8.299
r_long_range_B_other6.35
r_long_range_B_refined6.349
r_mcangle_it3.607
r_mcangle_other3.607
r_scangle_other3.52
r_scbond_it2.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.384
r_dihedral_angle_4_deg22.155
r_dihedral_angle_3_deg16.224
r_dihedral_angle_1_deg8.299
r_long_range_B_other6.35
r_long_range_B_refined6.349
r_mcangle_it3.607
r_mcangle_other3.607
r_scangle_other3.52
r_scbond_it2.257
r_scbond_other2.256
r_mcbond_it2.253
r_mcbond_other2.252
r_angle_refined_deg1.686
r_angle_other_deg0.813
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms3970
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms77

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
xia2data reduction
Aimlessdata scaling