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Crystal structure of the liganded form of Thermotoga maritima glucose binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DRI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 17% PEG 3350, 0.2M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.83 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.2 α = 90 b = 46.06 β = 108.22 c = 118.4 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 CCD ADSC QUANTUM 315 2005-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0357 NSLS X25
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 1.7 50 95.1 0.058 3.2 79951 79951
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.74 88.9 0.393 2.2 2.8 5488
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 2DRI 1.7 50 75919 4030 95.08 0.20502 0.20306 0.2105 0.24108 0.2481 RANDOM 25.765
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] -0.49 -0.14 -0.2 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.349 r_dihedral_angle_4_deg 13.867 r_dihedral_angle_3_deg 13.386 r_dihedral_angle_1_deg 5.511 r_scangle_it 2.242 r_scbond_it 1.585 r_angle_refined_deg 1.172 r_mcangle_it 0.989 r_mcbond_it 0.914 r_angle_other_deg 0.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.349 r_dihedral_angle_4_deg 13.867 r_dihedral_angle_3_deg 13.386 r_dihedral_angle_1_deg 5.511 r_scangle_it 2.242 r_scbond_it 1.585 r_angle_refined_deg 1.172 r_mcangle_it 0.989 r_mcbond_it 0.914 r_angle_other_deg 0.763 r_symmetry_vdw_other 0.297 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.198 r_nbtor_refined 0.17 r_nbd_other 0.166 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.142 r_mcbond_other 0.137 r_nbtor_other 0.082 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4725 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data scaling AMoRE phasing