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Structure of M. laminosus Ferredoxin with a shorter L1,2 loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 19% PEG 4000, 0.1M Tris buffer pH 7.2, 0.1M-0.18M Mg(NO3)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.997 α = 90 b = 58.997 β = 90 c = 55.898 γ = 90
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 4r optical hatch 2004-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 58.72 97.4 10318 2.8
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 1RFK 2.3 58.72 7805 412 95.06 0.22266 0.21902 0.2171 0.28751 0.287 RANDOM 53.776
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] 1.82 1.82 -3.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.303 r_dihedral_angle_3_deg 17.439 r_dihedral_angle_4_deg 11.131 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.998 r_scbond_it 2.345 r_angle_refined_deg 1.703 r_mcangle_it 1.656 r_mcbond_it 0.867 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.303 r_dihedral_angle_3_deg 17.439 r_dihedral_angle_4_deg 11.131 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.998 r_scbond_it 2.345 r_angle_refined_deg 1.703 r_mcangle_it 1.656 r_mcbond_it 0.867 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 1424 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling