X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.628830% PEG4000, 0.1M Na Citrate
Crystal Properties
Matthews coefficientSolvent content
2.2846.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 227.69α = 90
b = 63.15β = 114.72
c = 148.19γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87260ESRFID23-2

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
135099.70.10910.13.838803
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)
133.21.1281.133.86756

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 REPLACEMENTTHROUGHOUT5LRB349.3937637116599.820.196260.194830.24286RANDOM90.192
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]
-1-1.363.07-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.504
r_dihedral_angle_3_deg17.224
r_dihedral_angle_4_deg16.753
r_long_range_B_refined6.205
r_long_range_B_other6.203
r_dihedral_angle_1_deg5.865
r_scangle_other2.935
r_mcangle_it2.661
r_mcangle_other2.661
r_scbond_it1.736
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.504
r_dihedral_angle_3_deg17.224
r_dihedral_angle_4_deg16.753
r_long_range_B_refined6.205
r_long_range_B_other6.203
r_dihedral_angle_1_deg5.865
r_scangle_other2.935
r_mcangle_it2.661
r_mcangle_other2.661
r_scbond_it1.736
r_scbond_other1.736
r_mcbond_it1.59
r_mcbond_other1.59
r_angle_refined_deg1.158
r_angle_other_deg0.791
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
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 Atoms13424
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms166

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing