X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LS6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293The protein was concentrated to 33mg.mL-1. Condition: 18-22% (w/v) PEG 3350 and 50mM Tris-HCL buffer pH 8. Crystals appeared after two days at 293 K. , VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1542.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.86α = 90
b = 71.54β = 90
c = 122.77γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic confocal mirrors2011-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.548.8597.80.12610.624.91210702078733

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1LS62.548.85210701974610401000.210290.208350.24712RANDOM18.119
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]
-0.010.05-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.671
r_dihedral_angle_4_deg13.289
r_dihedral_angle_3_deg13.059
r_dihedral_angle_1_deg3.813
r_scangle_it3.713
r_scbond_it2.352
r_mcangle_it1.444
r_angle_other_deg1.141
r_mcbond_it0.775
r_angle_refined_deg0.587
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.671
r_dihedral_angle_4_deg13.289
r_dihedral_angle_3_deg13.059
r_dihedral_angle_1_deg3.813
r_scangle_it3.713
r_scbond_it2.352
r_mcangle_it1.444
r_angle_other_deg1.141
r_mcbond_it0.775
r_angle_refined_deg0.587
r_mcbond_other0.115
r_chiral_restr0.039
r_bond_refined_d0.003
r_gen_planes_refined0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4702
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms82

Software

Software
Software NamePurpose
StructureStudiodata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling