5OU5

Crystal structure of maize chloroplastic photosynthetic NADP(+)-dependent malic enzyme


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2850.1 M KCl, 0.1 M sodium citrate pH 5.5, 34 % (v/v) pentaerythritol-propylate (5/4 PO/OH)
Crystal Properties
Matthews coefficientSolvent content
2.5752.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.961α = 90
b = 147.155β = 90
c = 261.615γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.976254ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.248.881000.063460.99918.675.9132077
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.279990.47170.9063.516

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.248.88125428672599.470.16230.159710.21056RANDOM39.937
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]
-1.690.511.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.02
r_dihedral_angle_4_deg19.437
r_dihedral_angle_3_deg15.962
r_long_range_B_other8.376
r_long_range_B_refined8.374
r_scangle_other6.997
r_dihedral_angle_1_deg6.605
r_scbond_it4.564
r_scbond_other4.563
r_mcangle_it4.394
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.02
r_dihedral_angle_4_deg19.437
r_dihedral_angle_3_deg15.962
r_long_range_B_other8.376
r_long_range_B_refined8.374
r_scangle_other6.997
r_dihedral_angle_1_deg6.605
r_scbond_it4.564
r_scbond_other4.563
r_mcangle_it4.394
r_mcangle_other4.393
r_mcbond_it3.231
r_mcbond_other3.231
r_angle_refined_deg1.837
r_angle_other_deg1.077
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17295
Nucleic Acid Atoms
Solvent Atoms729
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing