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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 20% PEG 6000, 50mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.02 39.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.305 α = 90 b = 36.586 β = 106.92 c = 65.029 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 4 2006-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
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 1.15 50 99.5 0.063 11.8 3.3 97506 97506
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) 1.15 1.19 97.9 0.284 3.3 2.5 9495
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 1.15 50 97478 97478 4875 99.41 0.153 0.153 0.153 0.1595 0.168 0.1756 RANDOM 7.754
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] 0.07 0.12 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.111 r_dihedral_angle_3_deg 11.226 r_dihedral_angle_4_deg 8.562 r_dihedral_angle_1_deg 5.371 r_sphericity_free 3.803 r_scangle_it 2.555 r_sphericity_bonded 2.079 r_scbond_it 1.777 r_mcangle_it 1.25 r_angle_refined_deg 1.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.111 r_dihedral_angle_3_deg 11.226 r_dihedral_angle_4_deg 8.562 r_dihedral_angle_1_deg 5.371 r_sphericity_free 3.803 r_scangle_it 2.555 r_sphericity_bonded 2.079 r_scbond_it 1.777 r_mcangle_it 1.25 r_angle_refined_deg 1.244 r_angle_other_deg 0.881 r_mcbond_it 0.873 r_rigid_bond_restr 0.788 r_mcbond_other 0.333 r_symmetry_vdw_other 0.231 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.215 r_nbd_other 0.175 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.113 r_metal_ion_refined 0.087 r_nbtor_other 0.085 r_chiral_restr 0.077 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 2469 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction AMoRE phasing