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Crystal structure of the pre-B cell receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IT9 PDB ENTRIES 1IT9 AND 1ADQ experimental model PDB 1ADQ PDB ENTRIES 1IT9 AND 1ADQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 293 12% MP5K, 200mM Zinc acetate, 100mM PIPES, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.69 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.502 α = 90 b = 71.502 β = 90 c = 217.932 γ = 90
Symmetry Space Group P 43 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 ADSC QUANTUM 4 2002-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 60 99.9 0.07 7 8.1 16403
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 100 0.368 2 8.5
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 (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 ENTRIES 1IT9 AND 1ADQ 2.7 20 14658 15425 824 99.7 0.269 0.267 0.2593 0.295 0.2927 RANDOM 70.8
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] 2.73 2.73 -5.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.031 r_dihedral_angle_3_deg 18.617 r_dihedral_angle_4_deg 14.688 r_dihedral_angle_1_deg 4.46 r_scangle_it 2.784 r_scbond_it 1.918 r_mcangle_it 1.364 r_angle_refined_deg 1.272 r_mcbond_it 0.926 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.031 r_dihedral_angle_3_deg 18.617 r_dihedral_angle_4_deg 14.688 r_dihedral_angle_1_deg 4.46 r_scangle_it 2.784 r_scbond_it 1.918 r_mcangle_it 1.364 r_angle_refined_deg 1.272 r_mcbond_it 0.926 r_nbtor_refined 0.314 r_nbd_refined 0.268 r_symmetry_hbond_refined 0.253 r_symmetry_metal_ion_refined 0.25 r_metal_ion_refined 0.242 r_symmetry_vdw_refined 0.23 r_xyhbond_nbd_refined 0.216 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3427 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PHASER phasing CNS refinement HKL-2000 data scaling ADSC data collection