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crystal structure of human GITRL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.2M Lithium sulfate, 0.1M Tris, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.07 40.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.413 α = 90 b = 46.384 β = 91.56 c = 76.46 γ = 90
Symmetry Space Group C 1 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 100 IMAGE PLATE RIGAKU RAXIS IV 2006-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 75 96.9 0.08 0.08 127.9 5 16716 16198 5 3
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) Redundancy Number Unique Reflections (All) 1 2.2 2.28 87.8 0.547 0.547 5.8 3.5 1627
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.2 75 16716 16198 1012 90.76 0.20872 0.20394 0.1972 0.27992 0.2659 RANDOM 42.022
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] -1.68 -0.38 2.71 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.06 r_dihedral_angle_3_deg 21.583 r_dihedral_angle_4_deg 13.064 r_dihedral_angle_1_deg 10.364 r_scangle_it 4.256 r_scbond_it 3.067 r_angle_refined_deg 2.521 r_mcangle_it 2.091 r_mcbond_it 1.347 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.06 r_dihedral_angle_3_deg 21.583 r_dihedral_angle_4_deg 13.064 r_dihedral_angle_1_deg 10.364 r_scangle_it 4.256 r_scbond_it 3.067 r_angle_refined_deg 2.521 r_mcangle_it 2.091 r_mcbond_it 1.347 r_nbtor_refined 0.326 r_nbd_refined 0.266 r_symmetry_vdw_refined 0.239 r_xyhbond_nbd_refined 0.219 r_symmetry_hbond_refined 0.182 r_chiral_restr 0.18 r_bond_refined_d 0.025 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2515 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement