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Desmethyl-4-deoxygadusol synthase from Anabaena variabilis (Ava_3858) with NAD+ and Zn2+ bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 5% PEG 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.5 α = 90 b = 120.261 β = 90 c = 133.26 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 103 CCD ADSC QUANTUM 315r 2014-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.7 66.63 99.9 0.995 9.5 27.5 118029
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4P53 1.7 66.63 1.33 117877 5828 99.9 0.1574 0.1561 0.1833 0.1602
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 14.309 f_angle_d 0.95 f_chiral_restr 0.054 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6363 Nucleic Acid Atoms Solvent Atoms 1294 Heterogen Atoms 146
Software Software Software Name Purpose PHENIX refinement Aimless data scaling MR-Rosetta phasing iMOSFLM data reduction