3DGN

A non-biological ATP binding protein crystallized in the presence of 100 mM ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop vapor diffusion8.52980.1 M sodium phosphate, 0.25 M sodium citrate, 0.3 M sodium chloride, 23% polyethylene glycol 400, 0.2 M ammonium acetate, pH 8.5, sitting drop vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.3871.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.383α = 90
b = 72.383β = 90
c = 54.777γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray143IMAGE PLATERIGAKU RAXIS IV++mirrors2008-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE1.5418

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
12.72599.10.28356.54736
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.899.86.5469

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 REPLACEMENTTHROUGHOUT2.723.7472021599.010.20.1970.255RANDOM27.778
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]
0.10.050.1-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.095
r_dihedral_angle_3_deg18.193
r_dihedral_angle_4_deg9.264
r_dihedral_angle_1_deg8.504
r_scangle_it6.113
r_scbond_it3.704
r_angle_refined_deg2.955
r_mcangle_it2.169
r_mcbond_it1.148
r_chiral_restr0.196
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.095
r_dihedral_angle_3_deg18.193
r_dihedral_angle_4_deg9.264
r_dihedral_angle_1_deg8.504
r_scangle_it6.113
r_scbond_it3.704
r_angle_refined_deg2.955
r_mcangle_it2.169
r_mcbond_it1.148
r_chiral_restr0.196
r_bond_refined_d0.033
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms587
Nucleic Acid Atoms
Solvent Atoms33
Heterogen Atoms42

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling