X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TNFPDB ENTRY 2TNF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.529810 MM CACL2, 100 MM TRIS, PH 8.50, 20% METHONAL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
3.4864.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.404α = 90
b = 120.404β = 90
c = 120.404γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2007-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.55099.90.170.1243.521.11085654.5
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)
12.52.591000.560.961.710.6

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 2TNF2.519.81046232399.980.210850.209290.26336RANDOM51.137
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.538
r_dihedral_angle_3_deg20.234
r_dihedral_angle_4_deg17.171
r_scangle_it14.697
r_scbond_it11.975
r_mcangle_it11.473
r_dihedral_angle_1_deg11.062
r_mcbond_it9.372
r_angle_refined_deg2.355
r_nbtor_refined0.355
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.538
r_dihedral_angle_3_deg20.234
r_dihedral_angle_4_deg17.171
r_scangle_it14.697
r_scbond_it11.975
r_mcangle_it11.473
r_dihedral_angle_1_deg11.062
r_mcbond_it9.372
r_angle_refined_deg2.355
r_nbtor_refined0.355
r_symmetry_hbond_refined0.289
r_xyhbond_nbd_refined0.255
r_nbd_refined0.244
r_symmetry_vdw_refined0.178
r_chiral_restr0.142
r_bond_refined_d0.027
r_gen_planes_refined0.009
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 Atoms1121
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms1

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling