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Crystal structure of a disulfide mutant glucose binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 0.1M HEPES, pH7.5, 20% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.07 40.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.84 α = 90 b = 36.68 β = 124.03 c = 79.07 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 MARRESEARCH 2006-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 1.2 50 91.6 0.054 13.17 81424 81424 -3 16.267
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 1.3 72 0.262 3.7 13552
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2HPH 1.2 15 81403 81403 4070 100 0.168 0.168 0.167 0.1733 0.191 0.1937 RANDOM 11.115
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] -0.17 0.31 0.97 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.238 r_dihedral_angle_3_deg 11.568 r_dihedral_angle_4_deg 9.987 r_dihedral_angle_1_deg 5.454 r_sphericity_free 3.631 r_scangle_it 2.616 r_sphericity_bonded 2.19 r_scbond_it 1.831 r_mcangle_it 1.3 r_angle_refined_deg 1.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.238 r_dihedral_angle_3_deg 11.568 r_dihedral_angle_4_deg 9.987 r_dihedral_angle_1_deg 5.454 r_sphericity_free 3.631 r_scangle_it 2.616 r_sphericity_bonded 2.19 r_scbond_it 1.831 r_mcangle_it 1.3 r_angle_refined_deg 1.196 r_rigid_bond_restr 0.948 r_mcbond_it 0.897 r_angle_other_deg 0.879 r_mcbond_other 0.379 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.197 r_nbd_other 0.176 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.158 r_symmetry_vdw_other 0.147 r_xyhbond_nbd_refined 0.131 r_nbtor_other 0.083 r_metal_ion_refined 0.081 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2538 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 13
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction AMoRE phasing