X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W88PDB ENTRY 2W88 CHAIN A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15% PEG 8K, 0.1M ZINC ACETATE, 0.2 M SODIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.5652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.74α = 90
b = 55.74β = 90
c = 197.85γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
11.846.999.10.068.65.420932-317.71
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)
11.81.993.70.292.75.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2W88 CHAIN A1.865.9419859107299.10.1760.1730.224RANDOM20.87
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]
1.270.631.27-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.374
r_dihedral_angle_3_deg12.531
r_dihedral_angle_4_deg10.64
r_dihedral_angle_1_deg5.923
r_scangle_it3.166
r_mcangle_it2.63
r_scbond_it2.61
r_mcbond_it1.755
r_angle_refined_deg1.274
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.374
r_dihedral_angle_3_deg12.531
r_dihedral_angle_4_deg10.64
r_dihedral_angle_1_deg5.923
r_scangle_it3.166
r_mcangle_it2.63
r_scbond_it2.61
r_mcbond_it1.755
r_angle_refined_deg1.274
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1626
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing