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Crystal structure of FAD-dependent dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IRN PDB entries 4IRN & 4ETW experimental model PDB 4ETW PDB entries 4IRN & 4ETW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 279 15 mM magnesium acetate, 50 mM sodium cacodylate, pH 6.0, 1.8 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.66 66.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.416 α = 90 b = 104.416 β = 90 c = 234.139 γ = 120
Symmetry Space Group P 64 2 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 QUANTUM 315r 2016-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 45 100 0.1 0.102 0.021 7.7 23.1 60078
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.645 0.66 0.139 0.971 22.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 4IRN & 4ETW 1.9 45 56340 1933 96.91 0.1828 0.18184 0.1833 0.21072 0.2106 RANDOM 30.042
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.73 r_dihedral_angle_4_deg 19.58 r_dihedral_angle_3_deg 14.196 r_long_range_B_refined 7.642 r_dihedral_angle_1_deg 6.283 r_mcangle_it 3.938 r_scbond_it 3.496 r_mcbond_it 2.794 r_angle_refined_deg 1.881 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.73 r_dihedral_angle_4_deg 19.58 r_dihedral_angle_3_deg 14.196 r_long_range_B_refined 7.642 r_dihedral_angle_1_deg 6.283 r_mcangle_it 3.938 r_scbond_it 3.496 r_mcbond_it 2.794 r_angle_refined_deg 1.881 r_chiral_restr 0.143 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 3415 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing