3BJO

Crystal structure of the C-terminal domain of a possible ATP-binding protein from Methanocaldococcus jannaschii DSM 2661


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62890.4M Magnesium formate, 0.1M Sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.3663.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.472α = 90
b = 83.264β = 90
c = 125.641γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2007-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97857APS19-ID

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
12.0534.7198.30.0837.66.71037710377
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)
12.052.188.30.6672.24.5632

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.0534.719885988548798.220.203450.203450.202750.21686RANDOM47.561
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]
0.19-0.580.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.862
r_dihedral_angle_4_deg25.717
r_dihedral_angle_3_deg16.157
r_dihedral_angle_1_deg5.902
r_scangle_it4.747
r_scbond_it3.093
r_mcangle_it1.79
r_angle_refined_deg1.519
r_mcbond_it1.077
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.862
r_dihedral_angle_4_deg25.717
r_dihedral_angle_3_deg16.157
r_dihedral_angle_1_deg5.902
r_scangle_it4.747
r_scbond_it3.093
r_mcangle_it1.79
r_angle_refined_deg1.519
r_mcbond_it1.077
r_nbtor_refined0.314
r_nbd_refined0.209
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.145
r_chiral_restr0.128
r_symmetry_hbond_refined0.12
r_bond_refined_d0.02
r_gen_planes_refined0.007
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 Atoms856
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing