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Structure of Aspartate-N-hydroxylase (FzmM)from Streptomyces sp. V2: complex with NADPH and L-aspartate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 9% PEG 4000, 1.2 M di-Na tartrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 244.591 α = 90 b = 244.591 β = 90 c = 128.114 γ = 120
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 2023-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.1 122.3 100 0.186 0.301 0.093 0.993 7.4 10.6 166781
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 2.1 2.14 100 1.8 2.439 0.736 0.473 10.9
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 (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 2.1 122.3 158494 8267 99.97 0.18045 0.17931 0.1885 0.20207 0.2077 RANDOM 33.891
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] -0.72 -0.36 -0.72 2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.992 r_dihedral_angle_4_deg 20.944 r_dihedral_angle_3_deg 14.71 r_long_range_B_refined 8.425 r_long_range_B_other 8.425 r_dihedral_angle_1_deg 7.092 r_scangle_other 6.912 r_scbond_it 4.731 r_scbond_other 4.73 r_mcangle_it 4.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.992 r_dihedral_angle_4_deg 20.944 r_dihedral_angle_3_deg 14.71 r_long_range_B_refined 8.425 r_long_range_B_other 8.425 r_dihedral_angle_1_deg 7.092 r_scangle_other 6.912 r_scbond_it 4.731 r_scbond_other 4.73 r_mcangle_it 4.457 r_mcangle_other 4.457 r_mcbond_it 3.133 r_mcbond_other 3.13 r_angle_refined_deg 1.97 r_angle_other_deg 1.384 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 9279 Nucleic Acid Atoms Solvent Atoms 796 Heterogen Atoms 285
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing