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Sulfolobus solfataricus Glucose Dehydrogenase 1 in complex with NADP
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 MM TRIS (PH 8.0), 4.5 % PROPAN-2-OL
Crystal Properties Matthews coefficient Solvent content 2.7 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.62 α = 90 b = 92.296 β = 90 c = 138.264 γ = 90
Symmetry Space Group P 21 21 2
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 2004-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.28 51.2 98.8 0.11 12.8 5.2 38690
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 2.28 2.4 99.6 0.26 6.3 5.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CD9 2.28 138.68 38076 2008 98.1 0.198 0.196 0.246 0.2609 RANDOM 20.24
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] -0.16 1.6 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.148 r_dihedral_angle_4_deg 20.855 r_dihedral_angle_3_deg 16.962 r_dihedral_angle_1_deg 7.531 r_scangle_it 3.782 r_scbond_it 2.512 r_angle_refined_deg 1.817 r_mcangle_it 1.688 r_mcbond_it 1.034 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.148 r_dihedral_angle_4_deg 20.855 r_dihedral_angle_3_deg 16.962 r_dihedral_angle_1_deg 7.531 r_scangle_it 3.782 r_scbond_it 2.512 r_angle_refined_deg 1.817 r_mcangle_it 1.688 r_mcbond_it 1.034 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.219 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 5657 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement AMoRE phasing