2P65 | pdb_00002p65

Crystal Structure of the first nucleotide binding domain of chaperone ClpB1, putative, (Pv089580) from Plasmodium Vivax


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JBK1JBK.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52981.4 M Sodium Citrate 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8633.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.728α = 90
b = 52.213β = 90
c = 91.92γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.792.0693.80.090.09219.16.31761116520
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)
1.71.7667.40.340.3255.085.11167

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JBK.pdb1.792.06167111567084193.770.202950.202950.201030.20.239270.24RANDOM21.753
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]
-0.691.35-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.962
r_dihedral_angle_4_deg18.827
r_dihedral_angle_3_deg14.315
r_dihedral_angle_1_deg5.208
r_scangle_it2.514
r_scbond_it1.572
r_angle_refined_deg1.074
r_mcangle_it0.828
r_mcbond_it0.54
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.962
r_dihedral_angle_4_deg18.827
r_dihedral_angle_3_deg14.315
r_dihedral_angle_1_deg5.208
r_scangle_it2.514
r_scbond_it1.572
r_angle_refined_deg1.074
r_mcangle_it0.828
r_mcbond_it0.54
r_nbtor_refined0.297
r_nbd_refined0.191
r_symmetry_vdw_refined0.158
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_refined0.13
r_chiral_restr0.073
r_bond_refined_d0.007
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 Atoms1409
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing