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H-2Db complex with human gp100
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N5A PDB ENTRY 1N5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 10% PEG 6000, 0.1M Ammonium sulfate, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.2 α = 90 b = 165.4 β = 90 c = 161.3 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 210 2007-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1.91 24.82 93.1 71103 66186 1 1
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 1.91 2 65.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1N5A 1.91 24.81 1 66190 64542 3432 97.51 0.2351 0.22972 0.22762 0.2429 0.2683 0.2795 RANDOM 16.891
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.651 r_dihedral_angle_4_deg 20.119 r_dihedral_angle_3_deg 17.717 r_dihedral_angle_1_deg 6.337 r_mcangle_it 1.822 r_scangle_it 1.776 r_angle_refined_deg 1.442 r_mcbond_it 1.169 r_scbond_it 1.157 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.651 r_dihedral_angle_4_deg 20.119 r_dihedral_angle_3_deg 17.717 r_dihedral_angle_1_deg 6.337 r_mcangle_it 1.822 r_scangle_it 1.776 r_angle_refined_deg 1.442 r_mcbond_it 1.169 r_scbond_it 1.157 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.25 r_symmetry_hbond_refined 0.236 r_xyhbond_nbd_refined 0.232 r_chiral_restr 0.111 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6336 Nucleic Acid Atoms Solvent Atoms 607 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XSCALE data scaling PHASER phasing