2RJK

Crystal Structure of Human TL1A Extracellular Domain C95S Mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QE3PDB ENTRY 2QE3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529810 MM CACL2, 100 MM TRIS, PH 8.50, 20% METHONAL, VAPOR DIFFUSION, SITTING DROP, TEMPERATUR 290K, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
3.362.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.226α = 90
b = 118.226β = 90
c = 118.226γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2007-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.97910NSLSX29A

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
12.35099.90.0850.06240.52213160
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)
2.32.381000.8780.7833.3315.9

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 2QE32.325.81270540099.860.213320.211830.26507RANDOM52.622
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_deg36.718
r_dihedral_angle_4_deg19.813
r_dihedral_angle_3_deg14.989
r_scangle_it9.163
r_mcangle_it8.658
r_scbond_it8.231
r_dihedral_angle_1_deg7.963
r_mcbond_it5.839
r_angle_refined_deg1.682
r_nbtor_refined0.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.718
r_dihedral_angle_4_deg19.813
r_dihedral_angle_3_deg14.989
r_scangle_it9.163
r_mcangle_it8.658
r_scbond_it8.231
r_dihedral_angle_1_deg7.963
r_mcbond_it5.839
r_angle_refined_deg1.682
r_nbtor_refined0.324
r_symmetry_hbond_refined0.228
r_nbd_refined0.224
r_symmetry_vdw_refined0.204
r_xyhbond_nbd_refined0.193
r_chiral_restr0.129
r_bond_refined_d0.019
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 Atoms1140
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms

Software

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