2H39

Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z84PDB Entry: 1Z84

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29310 MG/ML PROTEIN, 20% PEG 2000, 0.2M SODIUM CHLORIDE, 0.10M MES-ACETATE, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.318α = 90
b = 95.454β = 90
c = 110.504γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUM-RMONTEL OPTICS2005-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1,22.2347.731000.191211.2811.7832389
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)
2.232.2599.90.67562.927.34840

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB Entry: 1Z842.2347.72732302163999.910.1790.17610.243418.776
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]
0.031-0.0310.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.761
r_dihedral_angle_4_deg25.756
r_dihedral_angle_3_deg14.842
r_dihedral_angle_1_deg6.73
r_scbond_it3.722
r_scangle_it2.784
r_mcangle_it2.73
r_angle_refined_deg1.664
r_mcbond_it1.516
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.761
r_dihedral_angle_4_deg25.756
r_dihedral_angle_3_deg14.842
r_dihedral_angle_1_deg6.73
r_scbond_it3.722
r_scangle_it2.784
r_mcangle_it2.73
r_angle_refined_deg1.664
r_mcbond_it1.516
r_nbtor_refined0.31
r_symmetry_vdw_refined0.287
r_nbd_refined0.201
r_symmetry_hbond_refined0.188
r_metal_ion_refined0.178
r_xyhbond_nbd_refined0.162
r_chiral_restr0.111
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4904
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms82

Software

Software
Software NamePurpose
SAINTdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction