X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OB3PDB entry 2OB3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1M Bis-Tris, 20% polyethylene glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0640.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.286α = 104.73
b = 45.338β = 93.4
c = 78.913γ = 97.65
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180IMAGE PLATERIGAKU RAXIS IVmirrors2007-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.83501000.080.06113.22.94715847158
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.831.91000.3440.31932.9

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 REPLACEMENTTHROUGHOUTPDB entry 2OB31.8320.494474444744241393.60.14310.140310.19557RANDOM15.991
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]
0.560.04-0.31-0.41-0.27-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.027
r_dihedral_angle_4_deg18.263
r_dihedral_angle_3_deg13.045
r_dihedral_angle_1_deg5.953
r_scangle_it2.175
r_mcangle_it1.558
r_angle_refined_deg1.419
r_scbond_it1.395
r_mcbond_it1.006
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.027
r_dihedral_angle_4_deg18.263
r_dihedral_angle_3_deg13.045
r_dihedral_angle_1_deg5.953
r_scangle_it2.175
r_mcangle_it1.558
r_angle_refined_deg1.419
r_scbond_it1.395
r_mcbond_it1.006
r_nbtor_refined0.302
r_nbd_refined0.198
r_symmetry_hbond_refined0.157
r_symmetry_vdw_refined0.149
r_xyhbond_nbd_refined0.138
r_chiral_restr0.11
r_metal_ion_refined0.077
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5116
Nucleic Acid Atoms
Solvent Atoms843
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing