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Crystal Structure of HLA-DP2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG4000, 300mM Sodium Chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.86 74.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.2823 α = 90 b = 157.2823 β = 90 c = 61.8048 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2 2 SYNCHROTRON APS BEAMLINE 19-ID 1.0 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.25 136.08 100 7.1 12053 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.283 89.1 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.25 50 11332 645 86.16 0.21865 0.21693 0.2279 0.25094 0.241 RANDOM 93.721
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] 5.94 2.97 5.94 -8.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.92 r_dihedral_angle_3_deg 21.43 r_dihedral_angle_4_deg 20.275 r_dihedral_angle_1_deg 6.719 r_scangle_it 1.661 r_angle_refined_deg 1.49 r_scbond_it 0.957 r_mcangle_it 0.672 r_mcbond_it 0.364 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.92 r_dihedral_angle_3_deg 21.43 r_dihedral_angle_4_deg 20.275 r_dihedral_angle_1_deg 6.719 r_scangle_it 1.661 r_angle_refined_deg 1.49 r_scbond_it 0.957 r_mcangle_it 0.672 r_mcbond_it 0.364 r_nbtor_refined 0.319 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.221 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.096 r_symmetry_hbond_refined 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 3114 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 42
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling