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Crystal structure of Bacillus megaterium glucose dehydrogenase 4 in complex with NADH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M sodium cacodylate pH 6.5, 0.2M magnesium chloride, 50% PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.017 α = 90 b = 128.082 β = 110.44 c = 64.745 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 270 2010-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.00000 Photon Factory AR-NE3A
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 50 98.4 0.064 19.81 3.7 32754
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 2.08 89.5 0.325 3.94 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 34.96 31074 1653 98.24 0.19294 0.19046 0.24065 0.229 RANDOM 35.374
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] 2.7 0.47 -0.32 -2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.931 r_dihedral_angle_4_deg 21.119 r_dihedral_angle_3_deg 13.837 r_dihedral_angle_1_deg 5.66 r_scangle_it 2.599 r_scbond_it 1.597 r_angle_refined_deg 1.191 r_mcangle_it 1.089 r_mcbond_it 0.605 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.931 r_dihedral_angle_4_deg 21.119 r_dihedral_angle_3_deg 13.837 r_dihedral_angle_1_deg 5.66 r_scangle_it 2.599 r_scbond_it 1.597 r_angle_refined_deg 1.191 r_mcangle_it 1.089 r_mcbond_it 0.605 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3974 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 44
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling