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F420-dependent glucose-6-phosphate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UNK D_1292141271
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 12% PEG4000, 0.1 M NaOAc pH 4.6, 0.2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.528 α = 90 b = 239.408 β = 108.588 c = 108.2 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 PIXEL DECTRIS PILATUS3 6M 2021-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.51 50 98 0.454 4.9 6.4 167400 36.4
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 2.51 2.67 94.1 2.209 0.8 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2.513 49.234 -3 167374 8203 98.094 0.232 0.2305 0.2305 0.2571 0.2572 39.419
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] -1.085 0.163 0.741 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.127 r_dihedral_angle_6_deg 13.927 r_dihedral_angle_2_deg 11.118 r_lrange_it 6.887 r_lrange_other 6.882 r_dihedral_angle_1_deg 6.709 r_scangle_it 5.074 r_scangle_other 5.057 r_mcangle_it 3.597 r_mcangle_other 3.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.127 r_dihedral_angle_6_deg 13.927 r_dihedral_angle_2_deg 11.118 r_lrange_it 6.887 r_lrange_other 6.882 r_dihedral_angle_1_deg 6.709 r_scangle_it 5.074 r_scangle_other 5.057 r_mcangle_it 3.597 r_mcangle_other 3.597 r_scbond_it 3.176 r_scbond_other 3.165 r_mcbond_it 2.237 r_mcbond_other 2.237 r_angle_refined_deg 1.672 r_angle_other_deg 0.551 r_symmetry_xyhbond_nbd_refined 0.319 r_nbd_other 0.281 r_symmetry_nbd_refined 0.266 r_nbd_refined 0.204 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.17 r_symmetry_xyhbond_nbd_other 0.096 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.073 r_ncsr_local_group_56 0.045 r_ncsr_local_group_52 0.043 r_ncsr_local_group_6 0.042 r_ncsr_local_group_25 0.041 r_ncsr_local_group_40 0.04 r_ncsr_local_group_11 0.038 r_ncsr_local_group_54 0.038 r_ncsr_local_group_16 0.037 r_ncsr_local_group_1 0.036 r_ncsr_local_group_33 0.036 r_ncsr_local_group_53 0.036 r_ncsr_local_group_21 0.035 r_ncsr_local_group_30 0.035 r_ncsr_local_group_46 0.035 r_ncsr_local_group_65 0.035 r_ncsr_local_group_14 0.034 r_ncsr_local_group_55 0.034 r_ncsr_local_group_58 0.034 r_ncsr_local_group_60 0.034 r_ncsr_local_group_66 0.034 r_ncsr_local_group_2 0.033 r_ncsr_local_group_4 0.033 r_ncsr_local_group_7 0.033 r_ncsr_local_group_28 0.033 r_ncsr_local_group_38 0.033 r_ncsr_local_group_45 0.033 r_ncsr_local_group_17 0.032 r_ncsr_local_group_22 0.032 r_ncsr_local_group_36 0.032 r_ncsr_local_group_3 0.031 r_ncsr_local_group_10 0.031 r_ncsr_local_group_19 0.031 r_ncsr_local_group_26 0.031 r_ncsr_local_group_43 0.031 r_ncsr_local_group_23 0.03 r_ncsr_local_group_63 0.03 r_ncsr_local_group_64 0.03 r_ncsr_local_group_9 0.029 r_ncsr_local_group_13 0.029 r_ncsr_local_group_29 0.029 r_ncsr_local_group_8 0.028 r_ncsr_local_group_51 0.028 r_ncsr_local_group_5 0.027 r_ncsr_local_group_12 0.027 r_ncsr_local_group_18 0.027 r_ncsr_local_group_31 0.027 r_ncsr_local_group_34 0.027 r_ncsr_local_group_37 0.027 r_ncsr_local_group_44 0.027 r_ncsr_local_group_59 0.027 r_ncsr_local_group_15 0.026 r_ncsr_local_group_49 0.026 r_ncsr_local_group_57 0.026 r_ncsr_local_group_47 0.025 r_ncsr_local_group_61 0.025 r_ncsr_local_group_39 0.024 r_ncsr_local_group_41 0.024 r_ncsr_local_group_20 0.023 r_ncsr_local_group_24 0.023 r_ncsr_local_group_42 0.023 r_ncsr_local_group_27 0.022 r_ncsr_local_group_35 0.021 r_ncsr_local_group_50 0.021 r_ncsr_local_group_32 0.019 r_ncsr_local_group_62 0.018 r_ncsr_local_group_48 0.017 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 32314 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing