X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DA0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP296100 mM Na2HPO4, 100 mM Tris, pH 8.0 and 48% PEG400 (v/v)
Crystal Properties
Matthews coefficientSolvent content
1.8734.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.12α = 90
b = 48.12β = 90
c = 111.333γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85095.415.64.622383

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 REPLACEMENTTHROUGHOUT2DA01.848.1221190116595.350.210680.208010.25986RANDOM48.008
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]
0.560.56-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.239
r_dihedral_angle_3_deg19.103
r_dihedral_angle_4_deg17.608
r_long_range_B_refined8.609
r_long_range_B_other8.607
r_dihedral_angle_1_deg7.822
r_scangle_other5.336
r_mcangle_it4.331
r_mcangle_other4.329
r_scbond_it3.265
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.239
r_dihedral_angle_3_deg19.103
r_dihedral_angle_4_deg17.608
r_long_range_B_refined8.609
r_long_range_B_other8.607
r_dihedral_angle_1_deg7.822
r_scangle_other5.336
r_mcangle_it4.331
r_mcangle_other4.329
r_scbond_it3.265
r_scbond_other3.259
r_mcbond_other2.583
r_mcbond_it2.582
r_angle_refined_deg1.999
r_angle_other_deg1.636
r_chiral_restr0.113
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.008
r_gen_planes_other0.008
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 Atoms1757
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing