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Crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I7H PDB ENTRY 1i7h
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.6M trisodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.23 61.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.575 α = 90 b = 87.575 β = 90 c = 73.139 γ = 120
Symmetry Space Group P 61 2 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 ADSC QUANTUM 315 2007-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 1.9 75.81 98.6 0.116 8.7 9.1 13390
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) 1.9 1.97 97.8 0.35 9 1285
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 PDB ENTRY 1i7h 1.9 37.92 12725 664 98.79 0.18341 0.18172 0.18 0.21562 0.2124 RANDOM 18.387
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] -0.29 -0.14 -0.29 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.39 r_dihedral_angle_3_deg 12.532 r_dihedral_angle_4_deg 8.818 r_dihedral_angle_1_deg 6.43 r_scangle_it 4.429 r_scbond_it 2.525 r_angle_refined_deg 1.558 r_mcangle_it 1.469 r_mcbond_it 0.764 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.39 r_dihedral_angle_3_deg 12.532 r_dihedral_angle_4_deg 8.818 r_dihedral_angle_1_deg 6.43 r_scangle_it 4.429 r_scbond_it 2.525 r_angle_refined_deg 1.558 r_mcangle_it 1.469 r_mcbond_it 0.764 r_nbtor_refined 0.302 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.167 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 841 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 6
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling