☰ Navigation Tabs
Crystal structure of ferredoxin-NADP+ oxidoreductase from bacillus subtilis (form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZBW PDB ENTRY 2ZBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M HEPES buffer (pH 7.5), 30% 1,2-propanediol, 20% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.9 α = 90 b = 135.724 β = 90 c = 39.191 γ = 90
Symmetry Space Group P 21 21 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 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 1.8 26.87 99.9 0.071 7 32363
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) 1.8 1.86 99.5 0.388 6.1
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 2ZBW 1.8 26.87 30707 1602 100 0.17023 0.16885 0.1749 0.19645 0.2006 RANDOM 24.212
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] 0.17 -0.71 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.807 r_dihedral_angle_3_deg 12.417 r_dihedral_angle_4_deg 8.977 r_dihedral_angle_1_deg 5.3 r_scangle_it 1.976 r_angle_refined_deg 1.253 r_scbond_it 1.237 r_angle_other_deg 0.799 r_mcangle_it 0.796 r_mcbond_it 0.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.807 r_dihedral_angle_3_deg 12.417 r_dihedral_angle_4_deg 8.977 r_dihedral_angle_1_deg 5.3 r_scangle_it 1.976 r_angle_refined_deg 1.253 r_scbond_it 1.237 r_angle_other_deg 0.799 r_mcangle_it 0.796 r_mcbond_it 0.422 r_symmetry_vdw_other 0.231 r_nbd_refined 0.195 r_nbd_other 0.176 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.133 r_symmetry_hbond_refined 0.131 r_symmetry_vdw_refined 0.117 r_metal_ion_refined 0.107 r_mcbond_other 0.091 r_nbtor_other 0.081 r_bond_refined_d 0.007 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 2570 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 103
Software Software Software Name Purpose BSS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling