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Structure of Aspartate-N-hydroxylase (FzmM)from Streptomyces sp. V2: complex with NADPH and Sulphate
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 7 293 0.1 M Hepes pH 7
1.6 M Ammonium sulphate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 243.681 α = 90 b = 243.681 β = 90 c = 126.298 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 EIGER X 4M 2022-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
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 2.54 80.98 99.1 0.194 0.203 0.061 0.996 10.1 10.8 91662
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 2.54 2.58 86.4 1.8 4.151 1.266 0.293 10.3
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 2.54 80.98 87155 4503 99.19 0.20603 0.20423 0.2114 0.24181 0.2445 RANDOM 49.772
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] -1.14 -0.57 -1.14 3.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.335 r_dihedral_angle_4_deg 20.435 r_dihedral_angle_3_deg 14.873 r_long_range_B_refined 8.92 r_long_range_B_other 8.884 r_dihedral_angle_1_deg 7.743 r_scangle_other 7.37 r_mcangle_it 5.598 r_mcangle_other 5.598 r_scbond_it 5.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.335 r_dihedral_angle_4_deg 20.435 r_dihedral_angle_3_deg 14.873 r_long_range_B_refined 8.92 r_long_range_B_other 8.884 r_dihedral_angle_1_deg 7.743 r_scangle_other 7.37 r_mcangle_it 5.598 r_mcangle_other 5.598 r_scbond_it 5.224 r_scbond_other 5.083 r_mcbond_it 3.935 r_mcbond_other 3.934 r_angle_refined_deg 1.708 r_angle_other_deg 1.3 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 9271 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 284
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing