2VE6

Crystal structure of a Murine MHC class I H2-Db molecule in complex with a photocleavable peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPCRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING-DROP, VAPOR-DIFFUSION METHOD WITH A WELL SOLUTION OF 15% (W/V) PEG 8000, 0.05 M K/NA PHOSPHATE, 50-100 MM BETA-OCTYL-GLUCOPYRANOSIDE AND 0.1 M CACODYLATE AT PH 6.4.
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.24α = 90
b = 103.87β = 90.83
c = 168.81γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
12.652096.60.089.7250561

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 1WBX2.6519.6648002255896.90.2370.2340.291RANDOM47.84
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]
0.530.922.57-3.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.274
r_dihedral_angle_3_deg14.541
r_dihedral_angle_4_deg12.842
r_dihedral_angle_1_deg5.136
r_angle_refined_deg0.895
r_angle_other_deg0.73
r_scangle_it0.372
r_scbond_it0.242
r_mcangle_it0.231
r_mcbond_it0.214
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.274
r_dihedral_angle_3_deg14.541
r_dihedral_angle_4_deg12.842
r_dihedral_angle_1_deg5.136
r_angle_refined_deg0.895
r_angle_other_deg0.73
r_scangle_it0.372
r_scbond_it0.242
r_mcangle_it0.231
r_mcbond_it0.214
r_nbtor_refined0.173
r_nbd_refined0.164
r_nbd_other0.161
r_symmetry_hbond_refined0.144
r_symmetry_vdw_other0.139
r_symmetry_vdw_refined0.116
r_xyhbond_nbd_refined0.105
r_nbtor_other0.084
r_chiral_restr0.055
r_bond_refined_d0.005
r_bond_other_d0.002
r_gen_planes_refined0.002
r_gen_planes_other0.001
r_scbond_other
r_symmetry_metal_ion_refined
r_metal_ion_refined
r_mcbond_other
r_xyhbond_nbd_other
r_mcangle_other
r_metal_ion_other
r_symmetry_metal_ion_other
r_symmetry_hbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12628
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing