☰ Navigation Tabs
Crystal structure of the minor ferredoxin from Thermosynechococcus elongatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AUI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100 mM HEPES (pH 7.5), 2.4 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.72 28.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.946 α = 90 b = 51.121 β = 116.15 c = 31.57 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2018-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.38 28.34 99.3 0.056 0.999 12.82 3.68 16325
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 1.38 1.47 98.9 0.585 0.718 2 3.62
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 THROUGHOUT 5AUI 1.38 28.34 15531 793 99.7 0.1146 0.1124 0.1124 0.157 0.1567 RANDOM 18.168
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] -0.03 -0.32 1.18 -0.57
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.356 r_dihedral_angle_2_deg 37.032 r_dihedral_angle_3_deg 12.446 r_sphericity_bonded 10.86 r_dihedral_angle_4_deg 10.182 r_rigid_bond_restr 9.159 r_dihedral_angle_1_deg 6.448 r_angle_refined_deg 2.086 r_angle_other_deg 1.154 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.356 r_dihedral_angle_2_deg 37.032 r_dihedral_angle_3_deg 12.446 r_sphericity_bonded 10.86 r_dihedral_angle_4_deg 10.182 r_rigid_bond_restr 9.159 r_dihedral_angle_1_deg 6.448 r_angle_refined_deg 2.086 r_angle_other_deg 1.154 r_chiral_restr 0.132 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 821 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction