☰ Navigation Tabs
Structure of the M101A variant of the SidA ornithine hydroxylase complexed with NADP and the FAD in the "out" conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Enzyme stock solution: 8-10 mg/ml SidA (M101A) with 1 mM NADP+ in 25 mM HEPES (pH 7.5) and 100 mM NaCl. Crystallization reservoir: 17-21 % PEG-3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium acetate. Cryo-buffer: 15 % PEG-200, 20 % PEG 3350, 0.1 M HEPES, (pH 7.5), 0.1 M calcium acetate.
Drop ratio: 2 enzyme to 1 reservoir
Crystal Properties Matthews coefficient Solvent content 2.3 46.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.229 α = 90 b = 153.811 β = 109.28 c = 89.87 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2017-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0000 ALS 4.2.2
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 62.89 96.6 0.082 0.098 0.053 0.993 9.4 3.5 115533
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 95.9 0.445 0.546 0.31 0.74 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6X0I 2.1 62.89 1.35 112920 2208 94.43 0.2049 0.2042 0.2059 0.2406 0.2435 28.5864
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 f_dihedral_angle_d 19.925 f_angle_d 0.986 f_chiral_restr 0.056 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13765 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 438
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing