X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CFSPDB entry 3CFS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529825% PEG3350, 0.2M MgCl2, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
238.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.645α = 90
b = 87.214β = 90
c = 88.203γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.5418

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
12.388.0499.90.0920.4955.917716
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)
12.32.381000.8065.91728

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 3CFS2.3501771690399.650.2170.2140.261RANDOM28.577
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]
0.2-2.272.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.224
r_dihedral_angle_3_deg15.431
r_dihedral_angle_4_deg12.141
r_dihedral_angle_1_deg7.339
r_scangle_it3.272
r_scbond_it2.207
r_angle_refined_deg1.721
r_mcangle_it1.38
r_mcbond_it0.827
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.224
r_dihedral_angle_3_deg15.431
r_dihedral_angle_4_deg12.141
r_dihedral_angle_1_deg7.339
r_scangle_it3.272
r_scbond_it2.207
r_angle_refined_deg1.721
r_mcangle_it1.38
r_mcbond_it0.827
r_nbtor_refined0.3
r_nbd_refined0.223
r_symmetry_vdw_refined0.201
r_symmetry_hbond_refined0.166
r_xyhbond_nbd_refined0.157
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2582
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction