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Crystal structure of mutant AChBP in complex with glycine (T53F, Q74R, Y110A, I135S, G162E, S206CCP_KGTG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 Reservoir solution:2 M sodium formate, 0.1 M sodium acetate pH 4.6 .
Protein buffer: 50 mM tris, 250 mM NaCl, 0.1 M glycine
Crystal Properties Matthews coefficient Solvent content 2.63 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.919 α = 90 b = 100.266 β = 90 c = 165.238 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 CCD RIGAKU SATURN 944+ 2016-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54157
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 2.6 32.9 99.3 0.149 11.9 7.3 46736 17.9
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 2.6 2.69 99.5 0.632 3.2 7.3
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 5OAD 2.6 32.9 44310 2381 99.9 0.204 0.202 0.2064 0.235 0.2394 RANDOM 28.09
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] 0.6 -0.68 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.792 r_dihedral_angle_4_deg 22.767 r_dihedral_angle_3_deg 15.51 r_dihedral_angle_1_deg 6.478 r_long_range_B_refined 6.175 r_long_range_B_other 6.165 r_mcangle_it 3.484 r_mcangle_other 3.484 r_scangle_other 3.129 r_mcbond_it 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.792 r_dihedral_angle_4_deg 22.767 r_dihedral_angle_3_deg 15.51 r_dihedral_angle_1_deg 6.478 r_long_range_B_refined 6.175 r_long_range_B_other 6.165 r_mcangle_it 3.484 r_mcangle_other 3.484 r_scangle_other 3.129 r_mcbond_it 1.98 r_mcbond_other 1.98 r_scbond_it 1.798 r_scbond_other 1.798 r_angle_refined_deg 1.413 r_angle_other_deg 0.931 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.005 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 8351 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing