1ZD8

Structure of human adenylate kinase 3 like 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5291PEG 4000, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.652.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.128α = 90
b = 61.873β = 108.14
c = 50.192γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID1.0APS32-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
11.4847.6796.20.0533.839687396871119.3
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)
1.481.5383.60.2423.13406

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 1AKY1.4847.673957737693199496.920.225280.225280.224440.24019RANDOM19.391
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]
0.57-0.13-0.21-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_4_deg14.323
r_dihedral_angle_3_deg11.948
r_dihedral_angle_1_deg5.275
r_scangle_it3.476
r_scbond_it2.29
r_mcangle_it1.405
r_angle_refined_deg1.282
r_mcbond_it0.889
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_4_deg14.323
r_dihedral_angle_3_deg11.948
r_dihedral_angle_1_deg5.275
r_scangle_it3.476
r_scbond_it2.29
r_mcangle_it1.405
r_angle_refined_deg1.282
r_mcbond_it0.889
r_nbtor_refined0.307
r_nbd_refined0.206
r_symmetry_vdw_refined0.18
r_symmetry_hbond_refined0.12
r_xyhbond_nbd_refined0.116
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms1697
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms

Software

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