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Crystal structure of SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697 with a bound N(delta)-hydroxy-N(omega)-methyl-L-arginine intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M9S PDB entry 6M9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M Tris, pH 8.5, 0.1 M magnesium chloride, 14-20% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.19 43.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.95 α = 90 b = 107.73 β = 90 c = 150.54 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 CCD MARMOSAIC 300 mm CCD 2018-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.685 54.09 99.9 0.084 0.089 0.998 14.01 8.2 107050 24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.79 99.9 0.877 0.935 0.825 2.52 8.2
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 entry 6M9S 1.69 54.08 100867 5310 99.98 0.17121 0.17018 0.1813 0.19076 0.1983 RANDOM 33.041
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] 0.11 0.79 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.016 r_dihedral_angle_4_deg 17.628 r_dihedral_angle_3_deg 12.427 r_dihedral_angle_1_deg 5.051 r_long_range_B_refined 4.736 r_long_range_B_other 4.313 r_scangle_other 1.445 r_angle_refined_deg 1.172 r_mcangle_it 0.931 r_mcangle_other 0.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.016 r_dihedral_angle_4_deg 17.628 r_dihedral_angle_3_deg 12.427 r_dihedral_angle_1_deg 5.051 r_long_range_B_refined 4.736 r_long_range_B_other 4.313 r_scangle_other 1.445 r_angle_refined_deg 1.172 r_mcangle_it 0.931 r_mcangle_other 0.931 r_angle_other_deg 0.929 r_scbond_it 0.888 r_scbond_other 0.888 r_mcbond_it 0.579 r_mcbond_other 0.578 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 7303 Nucleic Acid Atoms Solvent Atoms 979 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing