X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W9I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527746% PEG200 (v/v) in 100 mM NaCl/1 mM MES, pH 6.5.
Crystal Properties
Matthews coefficientSolvent content
3.9869.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.114α = 90
b = 111.114β = 90
c = 137.09γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2012-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.4396.2399.90.050.0534.8535368
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.432.5297.25.52

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 REPLACEMENTTHROUGHOUT2W9I2.4396.2335110190999.060.174680.173030.2063RANDOM47.596
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]
0.170.090.17-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.981
r_dihedral_angle_4_deg13.398
r_dihedral_angle_3_deg12.25
r_dihedral_angle_1_deg5.736
r_long_range_B_refined3.859
r_long_range_B_other3.859
r_scangle_other1.853
r_mcangle_it1.549
r_mcangle_other1.549
r_scbond_it1.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.981
r_dihedral_angle_4_deg13.398
r_dihedral_angle_3_deg12.25
r_dihedral_angle_1_deg5.736
r_long_range_B_refined3.859
r_long_range_B_other3.859
r_scangle_other1.853
r_mcangle_it1.549
r_mcangle_other1.549
r_scbond_it1.136
r_scbond_other1.136
r_angle_refined_deg1.089
r_mcbond_it0.907
r_mcbond_other0.906
r_angle_other_deg0.895
r_chiral_restr0.116
r_bond_refined_d0.005
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 Atoms4206
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms325

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing