X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSelenomethionine derivative partially refined structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62770.1M Na Citrate, 0.2M K/Na Tartrate, 2M (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.550.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.157α = 90
b = 94.607β = 90
c = 130.583γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.3ALS5.0.3

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
11.65091.80.04724.12.8954219542111
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)
11.61.660.512.3

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 REPLACEMENTTHROUGHOUTSelenomethionine derivative partially refined structure1.65090414479091.750.195930.193830.23594RANDOM17.038
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]
0.72-0.33-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.372
r_dihedral_angle_4_deg17.367
r_dihedral_angle_3_deg14.089
r_dihedral_angle_1_deg5.722
r_scangle_it5.047
r_scbond_it3.448
r_mcangle_it3.251
r_mcbond_it2.379
r_angle_refined_deg1.564
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.372
r_dihedral_angle_4_deg17.367
r_dihedral_angle_3_deg14.089
r_dihedral_angle_1_deg5.722
r_scangle_it5.047
r_scbond_it3.448
r_mcangle_it3.251
r_mcbond_it2.379
r_angle_refined_deg1.564
r_nbtor_refined0.313
r_nbd_refined0.211
r_symmetry_vdw_refined0.172
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_refined0.15
r_chiral_restr0.1
r_bond_refined_d0.013
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_refined
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 Atoms5363
Nucleic Acid Atoms
Solvent Atoms709
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing