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Dark-operative protochlorophyllide oxidoreductase in the nucleotide-free form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 1 ul BchL protein in 100 mM HEPES pH 7.5, 150 mM NaCl, 10% (v/v) glycerol was mixed with 2 ul well solution containing 0.6 M sodium chloride, 0.1 M MES:NaOH pH 6.5, 20% (w/v) PEG 4000. Prior to freezing, the well solution was mixed in an equal volume of cryoprotectant solution with a final concentration of 9% (w/v) sucrose, 2% (w/v) glucose, 8% (v/v) glycerol, and 8% (v/v) ethylene glycol. Crystals were soaked for a few seconds in the cryoprotectant before being frozen in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 1.95 36.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.513 α = 90 b = 100.918 β = 99.27 c = 117.789 γ = 90
Symmetry Space Group I 1 2 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 PIXEL DECTRIS EIGER X 9M 2018-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 1.008 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 42.2 99.5 0.173 0.057 0.99 9.2 9.3 32733 80.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 95.3 0.908 0.413 0.573 1.5 5.1
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 MOLECULAR REPLACEMENT FREE R-VALUE 3FWY 2.6 41.71 1.34 32732 2873 99.41 0.2354 0.2314 0.2375 0.2772 0.2853 85.6
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 14.0058 f_angle_d 0.393 f_chiral_restr 0.0398 f_plane_restr 0.0034 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7648 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing