☰ Navigation Tabs
Open liganded crystal structure of xylose binding protein from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M9W PDB entry 3M9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 296 21%(w/v) polyethylene glycol 3350, 0.2M ammonium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.44 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.718 α = 90 b = 71.706 β = 100.51 c = 66.356 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 ADSC QUANTUM 210 2008-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 30 0.079 14880
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 2.1 2.21 0.363 2.2
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 3M9W 2.2 30 13126 696 84.46 0.19979 0.19679 0.1928 0.25573 0.2515 RANDOM 26.79
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] 0.1 0.61 -0.67 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.298 r_dihedral_angle_4_deg 18.41 r_dihedral_angle_3_deg 18.183 r_dihedral_angle_1_deg 5.56 r_scangle_it 4.143 r_scbond_it 2.513 r_mcangle_it 1.686 r_angle_refined_deg 1.633 r_mcbond_it 0.914 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.298 r_dihedral_angle_4_deg 18.41 r_dihedral_angle_3_deg 18.183 r_dihedral_angle_1_deg 5.56 r_scangle_it 4.143 r_scbond_it 2.513 r_mcangle_it 1.686 r_angle_refined_deg 1.633 r_mcbond_it 0.914 r_chiral_restr 0.114 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 2318 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 10
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling