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Crystal structure of Ferredoxin from Thermosynechococcus elongatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 2.6 M Ammonium sulfate, 0.2% benzamidine hydrochloride, 3% (w/v) 1,6-hexanediol
Crystal Properties Matthews coefficient Solvent content 2.26 45.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.441 α = 90 b = 53.314 β = 92.384 c = 32.278 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 PIXEL DECTRIS PILATUS 2M-F 2014-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1000 Photon Factory BL-1A
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 1.499 50 98.8 0.061 35.5 3.2 15300
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 1.499 1.53 93.6 0.291 3.9 3.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3B2G 1.499 32.25 15121 751 98.182 0.16 0.1589 0.1588 0.183 0.1842 RANDOM 21.24
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] 0.133 -0.064 -0.141 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.707 r_dihedral_angle_other_3_deg 28.314 r_dihedral_angle_3_deg 11.595 r_dihedral_angle_4_deg 8.565 r_dihedral_angle_1_deg 6.66 r_lrange_it 6.097 r_lrange_other 6.091 r_scangle_it 5.578 r_scangle_other 5.574 r_scbond_it 3.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.707 r_dihedral_angle_other_3_deg 28.314 r_dihedral_angle_3_deg 11.595 r_dihedral_angle_4_deg 8.565 r_dihedral_angle_1_deg 6.66 r_lrange_it 6.097 r_lrange_other 6.091 r_scangle_it 5.578 r_scangle_other 5.574 r_scbond_it 3.628 r_scbond_other 3.624 r_mcangle_other 2.792 r_mcangle_it 2.777 r_angle_refined_deg 1.984 r_mcbond_it 1.898 r_mcbond_other 1.824 r_angle_other_deg 1.529 r_dihedral_angle_other_2_deg 1.48 r_nbd_refined 0.206 r_symmetry_xyhbond_nbd_refined 0.198 r_nbd_other 0.186 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.112 r_chiral_restr 0.097 r_symmetry_nbd_refined 0.085 r_symmetry_nbtor_other 0.082 r_bond_other_d 0.018 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 749 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Coot model building HKL-2000 data reduction HKL-2000 data scaling