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Crystal structure of Aplysia ACHBP in complex with tropisetron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BYN PDB ENTRY 2BYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 22% PEG4000, 0.1 M TRIS-HCL PH 7.5, 0.2 M LI2SO4
Crystal Properties Matthews coefficient Solvent content 3.2 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.584 α = 90 b = 212.584 β = 90 c = 212.584 γ = 90
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 2006-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.2 87 100 0.09 13.9 5.8 80567 35.7
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 2.2 2.32 100 0.5 3.4 5.9
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 ENTRY 2BYN 2.2 75.16 78146 2420 99.95 0.17837 0.17732 0.193 0.21171 0.2223 RANDOM 37.5237
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.027 r_dihedral_angle_4_deg 22.446 r_dihedral_angle_3_deg 15.935 r_dihedral_angle_1_deg 6.201 r_scangle_it 2.778 r_scbond_it 1.951 r_angle_refined_deg 1.464 r_mcangle_it 1.175 r_mcbond_it 0.985 r_angle_other_deg 0.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.027 r_dihedral_angle_4_deg 22.446 r_dihedral_angle_3_deg 15.935 r_dihedral_angle_1_deg 6.201 r_scangle_it 2.778 r_scbond_it 1.951 r_angle_refined_deg 1.464 r_mcangle_it 1.175 r_mcbond_it 0.985 r_angle_other_deg 0.869 r_symmetry_vdw_other 0.25 r_nbd_other 0.205 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.18 r_nbtor_refined 0.178 r_mcbond_other 0.161 r_xyhbond_nbd_refined 0.153 r_nbtor_other 0.087 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_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 8491 Nucleic Acid Atoms Solvent Atoms 611 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing