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Crystal structure of ferredoxin-NADP+ oxidoreductase from Bacillus subtilis (FORM II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LZW PDB ENTRY 3LZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 20% PEG 3350, 0.2M Sodium fluoride, 5% Trehalose, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.68 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.466 α = 90 b = 64.85 β = 105.82 c = 61.116 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 CCD RIGAKU JUPITER 210 2008-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 26.85 96.9 0.051 3.6 59771
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 80.4 0.22 3
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 3LZW 1.9 26.85 56728 3014 100 0.18267 0.18113 0.1881 0.2111 0.2175 RANDOM 26.974
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] -1.37 -0.99 -0.31 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.38 r_dihedral_angle_4_deg 15.436 r_dihedral_angle_3_deg 12.673 r_dihedral_angle_1_deg 5.608 r_scangle_it 2.423 r_scbond_it 1.505 r_angle_refined_deg 1.325 r_mcangle_it 0.965 r_angle_other_deg 0.81 r_mcbond_it 0.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.38 r_dihedral_angle_4_deg 15.436 r_dihedral_angle_3_deg 12.673 r_dihedral_angle_1_deg 5.608 r_scangle_it 2.423 r_scbond_it 1.505 r_angle_refined_deg 1.325 r_mcangle_it 0.965 r_angle_other_deg 0.81 r_mcbond_it 0.513 r_symmetry_vdw_other 0.219 r_nbd_refined 0.189 r_symmetry_hbond_refined 0.189 r_nbd_other 0.182 r_nbtor_refined 0.174 r_metal_ion_refined 0.144 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.129 r_mcbond_other 0.107 r_nbtor_other 0.081 r_symmetry_vdw_refined 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5140 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 204
Software Software Software Name Purpose BSS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling