☰ Navigation Tabs
De Novo Photosynthetic Reaction Center Protein in Apo-State
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 4.8 277 24% w/v PEG1500, 100 mM CdCl2, 100 mM Na acetate, pH 4.8.
Cryoprotectant: 2-methyl-2.4-pentanediol
Crystal Properties Matthews coefficient Solvent content 1.7 27.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.692 α = 90 b = 23.693 β = 99.93 c = 72.756 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 RIGAKU SATURN 944+ Osmic VariMax mirror 2013-12-06 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) 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 1.78 18.46 95.1 0.047 17.12 3.4 14128 17.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.783 1.829 68.9 0.175 0.95 3.79
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5VJS 1.78 18.46 1.36 14127 722 95.19 0.1841 0.1828 0.1826 0.2086 0.2077 RANDOM 25.34
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 20.7003 f_angle_d 1.7819 f_chiral_restr 0.0817 f_bond_d 0.0137 f_plane_restr 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1572 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing