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Structural analysis of the choline binding protein ChoX in a semi-closed and ligand-free conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 ChoX crystals were obtained using the hanging drop method at 293 K, against a reservoir solution of 100 mM Na-acetate pH 4.8-5.0 and 15-25% polyethylene glycol 3350. , VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.9 57.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.1 α = 90 b = 232.5 β = 90.2 c = 47.3 γ = 90
Symmetry Space Group P 1 21 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 CCD MAR CCD 165 mm 2007-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.978 EMBL/DESY, HAMBURG BW7A
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 2.89 20 98.8 0.116 11 3.4 16055 38.22
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 2.9 3 99.4 0.421 2.8 3.4 1517
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 2RIN 2.89 19.47 15224 829 98.05 0.24461 0.24238 0.2753 0.28469 0.3232 RANDOM 5.617
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] 0.3 1.69 -22.98 22.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.328 r_dihedral_angle_4_deg 19.169 r_dihedral_angle_3_deg 16.746 r_dihedral_angle_1_deg 4.444 r_angle_refined_deg 1.161 r_scangle_it 0.329 r_scbond_it 0.2 r_mcangle_it 0.196 r_mcbond_it 0.108 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.328 r_dihedral_angle_4_deg 19.169 r_dihedral_angle_3_deg 16.746 r_dihedral_angle_1_deg 4.444 r_angle_refined_deg 1.161 r_scangle_it 0.329 r_scbond_it 0.2 r_mcangle_it 0.196 r_mcbond_it 0.108 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4352 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling