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Gluconobacter Ene-Reductase (GluER)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MYW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 100 MM SODIUM ACETATE MONOHYDRATE
PH 4.6, 150 MM AMMONIUM SULFATE, 25% (W/V) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.14 42.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.695 α = 90 b = 49.469 β = 90 c = 156.223 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 EIGER X 9M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.798 27.99 99.27 0.061 0.066 1 19.8 12.9 32965
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.798 1.83 1.235 0.557 0.924 1702
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 6MYW 1.798 27.99 31225 1669 99.27 0.17589 0.17346 0.1781 0.22285 0.2288 RANDOM 39.562
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] 7.56 -2.87 -4.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.523 r_dihedral_angle_4_deg 19.091 r_dihedral_angle_3_deg 15.526 r_long_range_B_refined 8.191 r_long_range_B_other 8.189 r_dihedral_angle_1_deg 7.223 r_scangle_other 5.356 r_mcangle_it 4.521 r_mcangle_other 4.52 r_scbond_it 3.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.523 r_dihedral_angle_4_deg 19.091 r_dihedral_angle_3_deg 15.526 r_long_range_B_refined 8.191 r_long_range_B_other 8.189 r_dihedral_angle_1_deg 7.223 r_scangle_other 5.356 r_mcangle_it 4.521 r_mcangle_other 4.52 r_scbond_it 3.806 r_scbond_other 3.805 r_mcbond_it 3.273 r_mcbond_other 3.224 r_angle_refined_deg 1.584 r_angle_other_deg 1.356 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2761 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX refinement PHASER phasing