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Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP and glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CD9 PDB ENTRY 2CD9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 % PEG 8000, 0.1 M TRIS (PH 8.0), 4.5 % (V/V) PROPAN-2-OL
Crystal Properties Matthews coefficient Solvent content 2.36 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.672 α = 90 b = 91.394 β = 90.03 c = 138.433 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 CCD 2005-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.6 41.2 96.5 0.05 13.9 2.2 203195
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 1.6 1.69 95.6 0.24 4.1 2.1
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 2CD9 1.6 138.68 216944 10908 96.4 0.192 0.19 0.1934 0.218 0.222 RANDOM 13.39
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] -0.057 0.831 -0.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.327 r_dihedral_angle_4_deg 17.826 r_dihedral_angle_3_deg 14.121 r_dihedral_angle_1_deg 5.751 r_scangle_it 2.622 r_scbond_it 1.745 r_angle_refined_deg 1.305 r_mcangle_it 1.078 r_mcbond_it 0.712 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.327 r_dihedral_angle_4_deg 17.826 r_dihedral_angle_3_deg 14.121 r_dihedral_angle_1_deg 5.751 r_scangle_it 2.622 r_scbond_it 1.745 r_angle_refined_deg 1.305 r_mcangle_it 1.078 r_mcbond_it 0.712 r_nbtor_refined 0.308 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.143 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11293 Nucleic Acid Atoms Solvent Atoms 1276 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing