X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EW1PDB entry 2EW1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529125% PEG8000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.855.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.447α = 90
b = 66.447β = 90
c = 145.116γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2006-06-27MSINGLE WAVELENGTH
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE1.54178

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
12.053099.90.1166.79.624106
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)
2.052.121000.9558.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE RPDB entry 2EW12.052023955201999.6880.2370.23310.2862thin shells24.248
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]
0.9840.4920.984-1.477
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.986
r_dihedral_angle_4_deg16.568
r_dihedral_angle_3_deg13.451
r_dihedral_angle_1_deg6.13
r_mcangle_it3.291
r_scangle_it3.087
r_mcbond_it2.402
r_scbond_it2.377
r_angle_refined_deg1.41
r_angle_other_deg0.966
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.986
r_dihedral_angle_4_deg16.568
r_dihedral_angle_3_deg13.451
r_dihedral_angle_1_deg6.13
r_mcangle_it3.291
r_scangle_it3.087
r_mcbond_it2.402
r_scbond_it2.377
r_angle_refined_deg1.41
r_angle_other_deg0.966
r_mcbond_other0.715
r_symmetry_vdw_other0.218
r_nbd_refined0.209
r_nbd_other0.199
r_nbtor_refined0.175
r_symmetry_vdw_refined0.164
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.131
r_nbtor_other0.085
r_chiral_restr0.077
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2455
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms61

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction