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
2.856.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.664α = 90
b = 126.664β = 90
c = 108.494γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-11-22MSINGLE 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
12.55098.40.0970.09741.29.2-353.3
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)
12.52.5489.50.5370.5372.8465.2

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 2o8n2.548.631144754297.520.1670.1650.219RANDOM59.071
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]
-0.26-0.13-0.260.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.814
r_dihedral_angle_3_deg18.141
r_dihedral_angle_4_deg15.795
r_dihedral_angle_1_deg6.178
r_scangle_it3.994
r_scbond_it2.738
r_angle_refined_deg1.805
r_mcangle_it1.489
r_angle_other_deg0.962
r_mcbond_it0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.814
r_dihedral_angle_3_deg18.141
r_dihedral_angle_4_deg15.795
r_dihedral_angle_1_deg6.178
r_scangle_it3.994
r_scbond_it2.738
r_angle_refined_deg1.805
r_mcangle_it1.489
r_angle_other_deg0.962
r_mcbond_it0.77
r_mcbond_other0.16
r_chiral_restr0.097
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1808
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms40

Software

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