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Crystal structure of an arabinose binding protein with designed serotonin binding site in open, ligand-free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ABP PDB ENTRY 5ABP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 20% PEG 3350, 0.2M (NH4)CITRATE, 2UMOL/ML SEROTONIN, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.76 α = 90 b = 86.3 β = 90 c = 116.82 γ = 90
Symmetry Space Group P 21 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 100 CCD MARRESEARCH 2008-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 40 99.6 0.17 14.8 7.27 41190 2 35.593
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 2.34 97.8 0.87 2.33 7.08
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 5ABP 2.2 37.96 2 39440 2093 99.84 0.21301 0.20994 0.2091 0.27159 0.2709 RANDOM 35.35
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] 0.01 -0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.717 r_dihedral_angle_4_deg 16.482 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_1_deg 5.637 r_scangle_it 3.269 r_scbond_it 1.965 r_mcangle_it 1.364 r_angle_refined_deg 1.248 r_mcbond_it 0.729 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.717 r_dihedral_angle_4_deg 16.482 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_1_deg 5.637 r_scangle_it 3.269 r_scbond_it 1.965 r_mcangle_it 1.364 r_angle_refined_deg 1.248 r_mcbond_it 0.729 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 4470 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling CCP4I phasing