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Structure of the Bet3-TPC6B core of TRAPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BJN PDB ENTRIES 2BJN, 1SZ7 experimental model PDB 1SZ7 PDB ENTRIES 2BJN, 1SZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 18-20% PEG 3500,0.2 M LI CITRATE
Crystal Properties Matthews coefficient Solvent content 2.2 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.45 α = 90 b = 69.59 β = 91.55 c = 144.006 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 110 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 2.3 20 95.6 0.05 13.76 3.46 29365 -3
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 2.3 2.44 90.1 0.34 3.7 3.46
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 2BJN, 1SZ7 2.3 20 28749 1513 100 0.223 0.221 0.2301 0.269 0.2764 RANDOM 56.35
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] 3.88 3.19 -1.05 -2.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.901 r_dihedral_angle_4_deg 19.235 r_dihedral_angle_3_deg 17.703 r_dihedral_angle_1_deg 8.774 r_scangle_it 1.672 r_angle_refined_deg 1.556 r_angle_other_deg 1.411 r_scbond_it 1.163 r_mcangle_it 0.602 r_mcbond_it 0.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.901 r_dihedral_angle_4_deg 19.235 r_dihedral_angle_3_deg 17.703 r_dihedral_angle_1_deg 8.774 r_scangle_it 1.672 r_angle_refined_deg 1.556 r_angle_other_deg 1.411 r_scbond_it 1.163 r_mcangle_it 0.602 r_mcbond_it 0.445 r_symmetry_hbond_refined 0.27 r_symmetry_vdw_other 0.218 r_nbd_refined 0.208 r_nbd_other 0.186 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_refined 0.136 r_nbtor_other 0.096 r_chiral_restr 0.086 r_bond_refined_d 0.017 r_bond_other_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4958 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing