9KK7 | pdb_00009kk7

Neutron structure of Ferredoxin-NADP+ reductase from maize root -Reduced 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 = 59.32α = 90
b = 59.32β = 90
c = 187.69γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11neutron100DIFFRACTOMETERiBIX2022-12-10LLAUE
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
11.819.42599.90.16690.96135.419.529336398
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)
11.81.860.72790.3668

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-VALUE5H591.819.42536397177199.660.1990.19710.246222.416
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]
-0.027-0.014-0.0270.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.538
r_dihedral_angle_3_deg15.5
r_dihedral_angle_other_6_deg13.899
r_dihedral_angle_2_deg7.013
r_dihedral_angle_1_deg6.344
r_lrange_it5.09
r_lrange_other4.794
r_dihedral_angle_other_3_deg3.796
r_scangle_other3.575
r_scangle_it3.414
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.538
r_dihedral_angle_3_deg15.5
r_dihedral_angle_other_6_deg13.899
r_dihedral_angle_2_deg7.013
r_dihedral_angle_1_deg6.344
r_lrange_it5.09
r_lrange_other4.794
r_dihedral_angle_other_3_deg3.796
r_scangle_other3.575
r_scangle_it3.414
r_scbond_other2.363
r_scbond_it2.285
r_mcangle_it2.224
r_mcangle_other2.223
r_angle_refined_deg1.783
r_mcbond_it1.566
r_mcbond_other1.565
r_angle_other_deg0.603
r_symmetry_nbd_refined0.311
r_nbd_refined0.237
r_nbd_other0.192
r_xyhbond_nbd_refined0.191
r_nbtor_refined0.188
r_symmetry_xyhbond_nbd_refined0.184
r_symmetry_nbd_other0.172
r_chiral_restr0.098
r_symmetry_nbtor_other0.042
r_gen_planes_refined0.011
r_bond_refined_d0.009
r_bond_other_d0.001
r_ext_dist_refined_b
r_gen_planes_other

Software

Software
Software NamePurpose
STARGazerdata reduction
STARGazerdata scaling
PHASERphasing
REFMACrefinement