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Neutron structure of Ferredoxin-NADP+ reductase from maize root -Oxidized form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H59
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293.15 PEG2000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.29 α = 90 b = 59.29 β = 90 c = 187.24 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 100 DIFFRACTOMETER iBIX 2022-03-02 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 2.05-5.38 JPARC MLF BL-03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 19.415 99.5 0.1548 0.9682 6.34 9.0226 36250
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 0.718 0.3492
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 (All) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B NEUTRON DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5H59 1.8 19.415 36248 1764 99.577 0.193 0.1904 0.2449 24.332
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] 0.043 0.022 0.043 -0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.481 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_other_6_deg 14.511 r_dihedral_angle_2_deg 8.061 r_dihedral_angle_1_deg 6.443 r_lrange_it 5.377 r_lrange_other 5.052 r_dihedral_angle_other_3_deg 3.895 r_scangle_other 3.895 r_scangle_it 3.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.481 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_other_6_deg 14.511 r_dihedral_angle_2_deg 8.061 r_dihedral_angle_1_deg 6.443 r_lrange_it 5.377 r_lrange_other 5.052 r_dihedral_angle_other_3_deg 3.895 r_scangle_other 3.895 r_scangle_it 3.696 r_scbond_other 2.529 r_scbond_it 2.428 r_mcangle_it 2.392 r_mcangle_other 2.392 r_mcbond_it 1.727 r_mcbond_other 1.727 r_angle_refined_deg 1.678 r_angle_other_deg 0.564 r_symmetry_nbd_refined 0.228 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.198 r_nbd_other 0.194 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.176 r_symmetry_nbd_other 0.163 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.053 r_gen_planes_refined 0.011 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_ext_dist_refined_b r_gen_planes_other
Software Software Software Name Purpose STARGazer data reduction STARGazer data scaling PHASER phasing REFMAC refinement