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Crystal structure of human rage ligand-binding domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M Na cacodylate, 0.2M Zn acetate, 11% PEG 8000, pH 6.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.7 54.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.85 α = 90 b = 119.96 β = 90 c = 28.89 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2006-08-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.008, 1.28, 1.283 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.85 35.18 99.8 0.09 11.38 23066 -3 33.657
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) 1 1.85 2 100 0.589 3.2
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 MAD THROUGHOUT 1.85 35 23063 1154 100 0.21 0.209 0.2093 0.24 0.2388 RANDOM 28.2
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] -1.02 -1.05 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.082 r_dihedral_angle_4_deg 24.105 r_dihedral_angle_3_deg 18.168 r_dihedral_angle_1_deg 8.127 r_scangle_it 4.466 r_scbond_it 2.695 r_angle_refined_deg 1.988 r_mcangle_it 1.876 r_mcbond_it 1.146 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.082 r_dihedral_angle_4_deg 24.105 r_dihedral_angle_3_deg 18.168 r_dihedral_angle_1_deg 8.127 r_scangle_it 4.466 r_scbond_it 2.695 r_angle_refined_deg 1.988 r_mcangle_it 1.876 r_mcbond_it 1.146 r_nbtor_refined 0.312 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.225 r_xyhbond_nbd_refined 0.212 r_symmetry_hbond_refined 0.204 r_metal_ion_refined 0.202 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1687 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 8
Software Software Software Name Purpose XSCALE data scaling SHELX phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction SHELXD phasing