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Amine Dehydrogenase from Cystobacter fuscus in complex with NADP+ and cyclohexylamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 2.0 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5; 10 mM NADP+; 20 mM cyclohexylamine
Crystal Properties Matthews coefficient Solvent content 2.14 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51 α = 90 b = 87 β = 90 c = 143 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 120 PIXEL DECTRIS PILATUS3 S 6M 2018-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.97 55.24 100 0.13 0.08 1 9.2 7.7 45901 19
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 1.97 2.02 0.75 0.43 0.85 2.4
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 6GET 1.97 55.24 43558 2265 99.95 0.19144 0.19008 0.1997 0.21734 0.221 RANDOM 25.738
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] -1.76 4.12 -2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_4_deg 17.105 r_dihedral_angle_3_deg 15.15 r_dihedral_angle_1_deg 7.168 r_long_range_B_refined 5.365 r_long_range_B_other 5.334 r_scangle_other 3.981 r_mcangle_it 3.207 r_mcangle_other 3.207 r_scbond_it 2.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_4_deg 17.105 r_dihedral_angle_3_deg 15.15 r_dihedral_angle_1_deg 7.168 r_long_range_B_refined 5.365 r_long_range_B_other 5.334 r_scangle_other 3.981 r_mcangle_it 3.207 r_mcangle_other 3.207 r_scbond_it 2.712 r_scbond_other 2.712 r_mcbond_it 2.213 r_mcbond_other 2.212 r_angle_refined_deg 1.684 r_angle_other_deg 1.452 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5055 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing