9KKC | pdb_00009kkc

Neutron structure of Ferredoxin-NADP+ reductase from maize root -Oxidized form


NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5H59 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE293.15PEG2000

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.29α = 90
b = 59.29β = 90
c = 187.24γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11neutron100DIFFRACTOMETERiBIX2022-03-02LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SPALLATION SOURCEJ-PARC MLF BEAMLINE BL-032.05-5.38JPARC MLFBL-03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.819.41599.50.15480.96826.349.022636250
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.860.7180.3492

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5H591.819.41536248176499.5770.1930.19040.244924.332
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]
0.0430.0220.043-0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.481
r_dihedral_angle_3_deg14.958
r_dihedral_angle_other_6_deg14.511
r_dihedral_angle_2_deg8.061
r_dihedral_angle_1_deg6.443
r_lrange_it5.377
r_lrange_other5.052
r_dihedral_angle_other_3_deg3.895
r_scangle_other3.895
r_scangle_it3.696
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.481
r_dihedral_angle_3_deg14.958
r_dihedral_angle_other_6_deg14.511
r_dihedral_angle_2_deg8.061
r_dihedral_angle_1_deg6.443
r_lrange_it5.377
r_lrange_other5.052
r_dihedral_angle_other_3_deg3.895
r_scangle_other3.895
r_scangle_it3.696
r_scbond_other2.529
r_scbond_it2.428
r_mcangle_it2.392
r_mcangle_other2.392
r_mcbond_it1.727
r_mcbond_other1.727
r_angle_refined_deg1.678
r_angle_other_deg0.564
r_symmetry_nbd_refined0.228
r_nbd_refined0.218
r_xyhbond_nbd_refined0.198
r_nbd_other0.194
r_nbtor_refined0.183
r_symmetry_xyhbond_nbd_refined0.176
r_symmetry_nbd_other0.163
r_chiral_restr0.088
r_symmetry_nbtor_other0.053
r_gen_planes_refined0.011
r_bond_refined_d0.008
r_bond_other_d0.001
r_ext_dist_refined_b
r_gen_planes_other

Software

Software
Software NamePurpose
STARGazerdata reduction
STARGazerdata scaling
PHASERphasing
REFMACrefinement