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F420-dependent glucose-6-phosphate dehydrogenase from Thermomicrobium roseus with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B4Y chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Crystallization: 16% PEG4000, 0.1 M Tris pH 8.5, 0.2 M NaOAc (Jena Bioscience screen 2, B2), Cryocondition: 15% PEG4000, 10% PEG400, 0.1 M Tris pH 8.5, 0.2 M NaOAc
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.767 α = 90 b = 154.89 β = 90 c = 173.459 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2020-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.22 50 99.8 0.107 13.4 6.7 117277 54.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.35 99.1 1.737 1 6.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.22 48.33 117277 5879 99.825 0.179 0.1777 0.1777 0.2102 0.2104 62.487
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] 1.882 0.844 -2.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.059 r_dihedral_angle_3_deg 13.659 r_dihedral_angle_2_deg 9.173 r_lrange_it 7.239 r_lrange_other 7.228 r_dihedral_angle_1_deg 6.5 r_scangle_it 4.988 r_scangle_other 4.987 r_mcangle_it 3.633 r_mcangle_other 3.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.059 r_dihedral_angle_3_deg 13.659 r_dihedral_angle_2_deg 9.173 r_lrange_it 7.239 r_lrange_other 7.228 r_dihedral_angle_1_deg 6.5 r_scangle_it 4.988 r_scangle_other 4.987 r_mcangle_it 3.633 r_mcangle_other 3.633 r_scbond_it 3.339 r_scbond_other 3.339 r_mcbond_it 2.562 r_mcbond_other 2.562 r_angle_refined_deg 1.601 r_angle_other_deg 0.536 r_symmetry_xyhbond_nbd_refined 0.297 r_symmetry_nbd_refined 0.296 r_nbd_other 0.271 r_nbd_refined 0.205 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_other 0.121 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.073 r_ncsr_local_group_11 0.05 r_ncsr_local_group_2 0.049 r_ncsr_local_group_4 0.049 r_ncsr_local_group_3 0.048 r_ncsr_local_group_5 0.048 r_ncsr_local_group_12 0.048 r_ncsr_local_group_6 0.046 r_ncsr_local_group_10 0.045 r_ncsr_local_group_13 0.045 r_ncsr_local_group_7 0.044 r_ncsr_local_group_8 0.044 r_ncsr_local_group_9 0.043 r_ncsr_local_group_14 0.043 r_ncsr_local_group_15 0.043 r_ncsr_local_group_1 0.04 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16011 Nucleic Acid Atoms Solvent Atoms 618 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing