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Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FWY PDB ENTRIES 3FWY AND 2XDQ experimental model PDB 2XDQ PDB ENTRIES 3FWY AND 2XDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 CRYSTALLIZED FROM 3% (W/V) PEG 6000, 100MM KCL, 100MM TRIS, PH 8.5; THEN SOAKED WITH 13% (W/V) PEG 8000, 100MM HEPES, PH 7.5, 15% (V/V) GLYCEROL, 5MM DTT, 0.01MM PCHLIDE, 24MM DMSO
Crystal Properties Matthews coefficient Solvent content 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 308.4 α = 90 b = 74.11 β = 91.24 c = 74.23 γ = 90
Symmetry Space Group C 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 CCD RAYONIX MIRRORS 2010-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 34.51 83.1 0.05 14.32 2.6 81370 3 23.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 48.2 0.26 3 0.6
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRIES 3FWY AND 2XDQ 2.1 34.51 1.99 81361 4028 83.09 0.2006 0.1989 0.2008 0.2331 0.2362 41.4
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 13.458 f_angle_d 1.018 f_chiral_restr 0.053 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11195 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 226
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing