☰ Navigation Tabs
Crystal structure of the RAG1 nonamer-binding domain with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNA PDB entry 3GNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.47 α = 90 b = 97.47 β = 90 c = 69.78 γ = 90
Symmetry Space Group I 4 2 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 ADSC QUANTUM 315r 2008-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.008 APS 24-ID-C
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 3 50 99.2 0.066 3382 1 1
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 3 3.11 100 0.239
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 3GNA 3 20 3382 158 99.41 0.24272 0.24165 0.2396 0.26739 RANDOM 46.72
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] 0.36 0.36 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.445 r_dihedral_angle_3_deg 15.234 r_dihedral_angle_4_deg 11.679 r_dihedral_angle_1_deg 3.592 r_angle_refined_deg 1.071 r_angle_other_deg 0.899 r_symmetry_vdw_other 0.232 r_nbd_refined 0.222 r_nbtor_refined 0.209 r_nbd_other 0.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.445 r_dihedral_angle_3_deg 15.234 r_dihedral_angle_4_deg 11.679 r_dihedral_angle_1_deg 3.592 r_angle_refined_deg 1.071 r_angle_other_deg 0.899 r_symmetry_vdw_other 0.232 r_nbd_refined 0.222 r_nbtor_refined 0.209 r_nbd_other 0.186 r_symmetry_hbond_refined 0.163 r_symmetry_vdw_refined 0.144 r_scangle_it 0.12 r_mcangle_it 0.112 r_mcbond_it 0.09 r_nbtor_other 0.082 r_scbond_it 0.082 r_xyhbond_nbd_refined 0.058 r_chiral_restr 0.053 r_mcbond_other 0.016 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 553 Nucleic Acid Atoms 548 Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing