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The crystal structure of a [3Fe-4S] ferredoxin associated with CYP194A4 from R. palustris HaA2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z8Q PDB ENTRY 2Z8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.3 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5, 2.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.87 34.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23.354 α = 90 b = 26.699 β = 90 c = 91.094 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC mirrors 2012-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.15 50 96.3 0.083 0.086 16.4 5.6 3425 3298 1 1 27.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 76.5 0.161 0.133 7.9 3.8 323
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2Z8Q 2.15 45.55 3246 3105 141 95.67 0.19591 0.19255 0.1961 0.27509 0.2647 RANDOM 27.635
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] -2.65 5.79 -3.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.928 r_dihedral_angle_3_deg 18.351 r_dihedral_angle_4_deg 18.293 r_dihedral_angle_1_deg 7.158 r_scangle_it 4.754 r_angle_refined_deg 3.077 r_scbond_it 2.881 r_mcangle_it 1.789 r_mcbond_it 0.98 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.928 r_dihedral_angle_3_deg 18.351 r_dihedral_angle_4_deg 18.293 r_dihedral_angle_1_deg 7.158 r_scangle_it 4.754 r_angle_refined_deg 3.077 r_scbond_it 2.881 r_mcangle_it 1.789 r_mcbond_it 0.98 r_chiral_restr 0.14 r_bond_refined_d 0.023 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 497 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 7
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling