2AZ1

Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NUEPDB ENTRY 1NUE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.2M CaCl2, 0.1M HEPES-Na, pH 7.5, 28% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8533.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.28α = 90
b = 108.7β = 90
c = 119.65γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
12.32099.10.099.312.9408704051454.98
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)
2.32.4497.20.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NUE2.35203637036283191899.760.220350.220350.216680.28944RANDOM47.772
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]
1.961.63-3.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.428
r_scangle_it3.811
r_scbond_it2.351
r_angle_refined_deg1.776
r_mcangle_it1.527
r_angle_other_deg0.977
r_mcbond_it0.84
r_symmetry_hbond_refined0.326
r_symmetry_vdw_refined0.307
r_xyhbond_nbd_refined0.254
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.428
r_scangle_it3.811
r_scbond_it2.351
r_angle_refined_deg1.776
r_mcangle_it1.527
r_angle_other_deg0.977
r_mcbond_it0.84
r_symmetry_hbond_refined0.326
r_symmetry_vdw_refined0.307
r_xyhbond_nbd_refined0.254
r_nbd_other0.247
r_nbd_refined0.227
r_symmetry_vdw_other0.203
r_metal_ion_refined0.154
r_chiral_restr0.106
r_nbtor_other0.095
r_bond_refined_d0.021
r_gen_planes_refined0.007
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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 Atoms7094
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
MOLREPphasing