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De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) cations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 277 1.2 M Li2SO4, 0.5 M (NH4)2SO4, 150 mM Na citrate, pH 5.9
Cryoprotectant: 28% glycerol, 1.25 M Li2SO4, 0.5 M (NH4)2SO4, 100 mM Na citrate, pH 5.85
Crystal Properties Matthews coefficient Solvent content 2.68 54.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.968 α = 90 b = 44.968 β = 90 c = 238.295 γ = 90
Symmetry Space Group P 41 21 2
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 RIGAKU SATURN 944+ Osmic VariMax mirror 2014-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 1.9 23.25 98.4 0.089 0.093 0.999 22.22 12.6 20059 28.22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 86.6 0.619 1.66
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 FREE R-VALUE 5VJS 1.9 23.25 19019 1014 98.26 0.22014 0.2189 0.2238 0.24336 0.2526 RANDOM 37.956
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] -0.07 -0.07 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.298 r_scangle_other 20.346 r_long_range_B_other 19.72 r_long_range_B_refined 19.628 r_scbond_it 18.459 r_scbond_other 18.377 r_dihedral_angle_3_deg 12.931 r_mcangle_other 10.677 r_mcangle_it 10.671 r_mcbond_it 9.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.298 r_scangle_other 20.346 r_long_range_B_other 19.72 r_long_range_B_refined 19.628 r_scbond_it 18.459 r_scbond_other 18.377 r_dihedral_angle_3_deg 12.931 r_mcangle_other 10.677 r_mcangle_it 10.671 r_mcbond_it 9.379 r_mcbond_other 9.334 r_dihedral_angle_4_deg 8.474 r_dihedral_angle_1_deg 3.554 r_angle_other_deg 0.976 r_angle_refined_deg 0.943 r_chiral_restr 0.045 r_bond_refined_d 0.005 r_gen_planes_other 0.003 r_gen_planes_refined 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1581 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing