2O67

Crystal structure of Arabidopsis thaliana PII bound to malonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O66pdb entry 2O66

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72982.5 M malonate, 0.1 M Na HEPES, pH 7.0, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8834.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.594α = 90
b = 66.726β = 118.41
c = 61.489γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic multilayer2006-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.52099.70.1040.10414.24.61146411464-341.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.5998.20.5170.5172.441139

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2O662.520109031090355299.630.204010.204010.200880.26567RANDOM44.622
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]
1.450.43-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.437
r_dihedral_angle_3_deg17.08
r_dihedral_angle_4_deg16.985
r_scangle_it5.268
r_dihedral_angle_1_deg5.15
r_scbond_it3.43
r_mcangle_it2.64
r_mcbond_it1.713
r_angle_refined_deg1.039
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.437
r_dihedral_angle_3_deg17.08
r_dihedral_angle_4_deg16.985
r_scangle_it5.268
r_dihedral_angle_1_deg5.15
r_scbond_it3.43
r_mcangle_it2.64
r_mcbond_it1.713
r_angle_refined_deg1.039
r_nbtor_refined0.297
r_nbd_refined0.178
r_symmetry_vdw_refined0.148
r_symmetry_hbond_refined0.127
r_xyhbond_nbd_refined0.12
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2477
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing