X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XEFpdb entry 1XEF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277Tris, PEG 6000, MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4449.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.142α = 90
b = 189.256β = 111.87
c = 63.475γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.72098.90.0946.826969265652
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7598.30.2575.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1XEF2.7205.226565140698.920.225990.223020.28022RANDOM51.569
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]
1.49-3.781.53-5.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.161
r_dihedral_angle_4_deg18.926
r_dihedral_angle_3_deg18.046
r_dihedral_angle_1_deg5.814
r_scangle_it1.248
r_angle_refined_deg1.214
r_scbond_it0.776
r_mcangle_it0.639
r_mcbond_it0.36
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.161
r_dihedral_angle_4_deg18.926
r_dihedral_angle_3_deg18.046
r_dihedral_angle_1_deg5.814
r_scangle_it1.248
r_angle_refined_deg1.214
r_scbond_it0.776
r_mcangle_it0.639
r_mcbond_it0.36
r_nbtor_refined0.303
r_nbd_refined0.196
r_symmetry_vdw_refined0.181
r_symmetry_hbond_refined0.167
r_xyhbond_nbd_refined0.127
r_chiral_restr0.077
r_bond_refined_d0.012
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7572
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing