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Aplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyridinyl)deschloroepibatidine analogue (2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 Reservoir: 0.2 M NaCl, 0.1 M Phosphate/citrate pH 4.2 8% PEG 8000
Buffer: 50 mM Tris 250 mM NaCl pH 7.5
Protein concentration: 4 mg/ml
Microseeded
Crystal Properties Matthews coefficient Solvent content 3.49 64.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.53 α = 90 b = 136.948 β = 102.74 c = 131.552 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 100 PIXEL DECTRIS PILATUS 6M-F 2017-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.968580 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.4 46.82 98.7 0.089 0.95 8.2 2.9 139199 29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 98.7 0.51 0.65 2.5 2.8
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 5o87 2.4 46.82 131926 6903 98.25 0.18893 0.18785 0.1934 0.21003 0.2152 RANDOM 34.364
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] -2.47 -0.22 3.82 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 16.194 r_dihedral_angle_3_deg 13.479 r_dihedral_angle_1_deg 8.064 r_long_range_B_refined 7.437 r_long_range_B_other 7.397 r_scangle_other 5.388 r_mcangle_it 3.638 r_mcangle_other 3.638 r_scbond_it 3.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 16.194 r_dihedral_angle_3_deg 13.479 r_dihedral_angle_1_deg 8.064 r_long_range_B_refined 7.437 r_long_range_B_other 7.397 r_scangle_other 5.388 r_mcangle_it 3.638 r_mcangle_other 3.638 r_scbond_it 3.307 r_scbond_other 3.307 r_mcbond_it 2.264 r_mcbond_other 2.264 r_angle_refined_deg 1.49 r_angle_other_deg 0.919 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16388 Nucleic Acid Atoms Solvent Atoms 924 Heterogen Atoms 610
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing