5JH2

Crystal structure of the holo form of AKR4C7 from maize


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JH1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2910,1 M Tris-HCl, pH, 6.0, 22% m/v PEG4000, 0,1 M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.0138.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.219α = 90
b = 55.857β = 90
c = 105.74γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.458LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.7252.8791.70.0690.0780.03411.64.82786427864
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.8174.80.6431.24.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5JH11.7249.3926401141291.250.170.1680.2071RANDOM27.406
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]
0.140.17-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.996
r_dihedral_angle_3_deg13.55
r_dihedral_angle_4_deg9.993
r_dihedral_angle_1_deg5.86
r_mcangle_it2.86
r_mcbond_it2.181
r_mcbond_other2.17
r_angle_refined_deg1.843
r_angle_other_deg1.025
r_chiral_restr0.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.996
r_dihedral_angle_3_deg13.55
r_dihedral_angle_4_deg9.993
r_dihedral_angle_1_deg5.86
r_mcangle_it2.86
r_mcbond_it2.181
r_mcbond_other2.17
r_angle_refined_deg1.843
r_angle_other_deg1.025
r_chiral_restr0.111
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2015
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms32

Software

Software
Software NamePurpose
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction