X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O8NPDB ENTRY 2O8N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62930.1 M SODIUM ACETATE, 1.5 M AMMONIUM SULFATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9558.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.209α = 90
b = 124.446β = 102.71
c = 164.249γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300MIRRORS2008-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.12712APS21-ID-D

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
12.115097.60.0870.08726.8264.1477756477756-3
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)
12.112.1583.30.5930.5932.5683.6

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 2O8N2.1150111053586497.80.178230.176510.2106RANDOM34.638
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]
5.044.49-3.50.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.676
r_dihedral_angle_4_deg15.295
r_dihedral_angle_3_deg14.741
r_dihedral_angle_1_deg6.224
r_scangle_it4.302
r_angle_other_deg4.049
r_scbond_it2.797
r_angle_refined_deg1.73
r_mcangle_it1.694
r_mcbond_it0.944
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.676
r_dihedral_angle_4_deg15.295
r_dihedral_angle_3_deg14.741
r_dihedral_angle_1_deg6.224
r_scangle_it4.302
r_angle_other_deg4.049
r_scbond_it2.797
r_angle_refined_deg1.73
r_mcangle_it1.694
r_mcbond_it0.944
r_chiral_restr0.105
r_bond_refined_d0.02
r_gen_planes_other0.01
r_gen_planes_refined0.009
r_bond_other_d
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10848
Nucleic Acid Atoms
Solvent Atoms477
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing