X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NXBPDB entry 2NXB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.20M Na/K tartrate, 20.0% PEG 3350, 10.0% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3447.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.935α = 90
b = 92.679β = 90
c = 100.107γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97866SLSX10SA

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
12.0550.06396.40.1290.1294.66.42587024939
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)
12.052.1677.60.6810.68112.92857

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2NXB2.0550.0632488324883124996.380.1940.1940.1910.259RANDOM22.732
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]
-0.790.540.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.254
r_dihedral_angle_3_deg14.656
r_scangle_it8.048
r_dihedral_angle_4_deg7.217
r_scbond_it6.922
r_dihedral_angle_1_deg5.799
r_mcangle_it4.772
r_mcbond_it4.141
r_mcbond_other1.974
r_angle_refined_deg1.517
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.254
r_dihedral_angle_3_deg14.656
r_scangle_it8.048
r_dihedral_angle_4_deg7.217
r_scbond_it6.922
r_dihedral_angle_1_deg5.799
r_mcangle_it4.772
r_mcbond_it4.141
r_mcbond_other1.974
r_angle_refined_deg1.517
r_angle_other_deg0.993
r_symmetry_vdw_refined0.295
r_symmetry_vdw_other0.263
r_nbd_refined0.193
r_nbtor_refined0.185
r_nbd_other0.178
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.15
r_nbtor_other0.091
r_chiral_restr0.086
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2562
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction