☰ Navigation Tabs
Crystal Structure of human GITRL mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 298 25% PEG 3350, 0.1M Sodium Acetate pH 4.5, Vapor diffusion, Sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.21 α = 90 b = 72.21 β = 90 c = 52.937 γ = 120
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 2006-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 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 3.2 29.8 96.7 0.141 0.116 6.4 2.7 2580 2580
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.2 3.31 97 0.56 2.7 260
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2q1m 3.2 29.8 2578 2578 120 96.95 0.183 0.183 0.18 0.1766 0.239 0.2289 RANDOM 47.137
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] 1.67 0.84 1.67 -2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.847 r_dihedral_angle_3_deg 21.656 r_dihedral_angle_4_deg 9.094 r_dihedral_angle_1_deg 8.776 r_mcangle_it 3.018 r_scangle_it 2.052 r_mcbond_it 1.775 r_scbond_it 1.292 r_angle_refined_deg 1.18 r_nbtor_refined 0.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.847 r_dihedral_angle_3_deg 21.656 r_dihedral_angle_4_deg 9.094 r_dihedral_angle_1_deg 8.776 r_mcangle_it 3.018 r_scangle_it 2.052 r_mcbond_it 1.775 r_scbond_it 1.292 r_angle_refined_deg 1.18 r_nbtor_refined 0.349 r_nbd_refined 0.256 r_symmetry_vdw_refined 0.255 r_xyhbond_nbd_refined 0.22 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 921 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction