3LTD

X-ray structure of a non-biological ATP binding protein determined at 2.8 A by multi-wavelength anomalous dispersion


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.1 M SODIUM PHOSPHATE PH 8.5, 0.25 M SODIUM CITRATE, 0.3 M SODIUM CHLORIDE, 23% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
4.3671.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.145α = 90
b = 73.145β = 90
c = 54.804γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-06-18MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12B1.2817, 1.2750, 1.2822NSLSX12B

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
12.85092.50.14812.693.34054
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)
2.82.994.30.5053.2

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 DIFFRACTIONMADTHROUGHOUT2.836.56405318892.50.1820.180.218RANDOM26.57
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]
0.070.030.07-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.49
r_dihedral_angle_3_deg17.143
r_dihedral_angle_4_deg10.198
r_dihedral_angle_1_deg6.062
r_scangle_it3.599
r_scbond_it2.078
r_angle_refined_deg1.742
r_mcangle_it1.28
r_mcbond_it0.646
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.49
r_dihedral_angle_3_deg17.143
r_dihedral_angle_4_deg10.198
r_dihedral_angle_1_deg6.062
r_scangle_it3.599
r_scbond_it2.078
r_angle_refined_deg1.742
r_mcangle_it1.28
r_mcbond_it0.646
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms583
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms43

Software

Software
Software NamePurpose
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling