2XUU

Crystal structure of a DAP-kinase 1 mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.2 M LISO4 0.1 M BIS-TRIS PH 5.5 25% PEG 4000 0.002% NAN3
Crystal Properties
Matthews coefficientSolvent content
2.4149.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.74α = 90
b = 84.43β = 90
c = 86.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2009-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
11.830.411000.119.34344692.516.5
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)
11.81.999.90.562.54

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2W4K1.860.3632678173699.940.17890.176380.22583RANDOM20.11
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]
-0.56-0.781.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.809
r_dihedral_angle_4_deg20.884
r_dihedral_angle_3_deg16.442
r_dihedral_angle_1_deg6.055
r_scangle_it5.774
r_scbond_it3.59
r_mcangle_it2.294
r_angle_refined_deg2.009
r_mcbond_it1.323
r_chiral_restr0.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.809
r_dihedral_angle_4_deg20.884
r_dihedral_angle_3_deg16.442
r_dihedral_angle_1_deg6.055
r_scangle_it5.774
r_scbond_it3.59
r_mcangle_it2.294
r_angle_refined_deg2.009
r_mcbond_it1.323
r_chiral_restr0.163
r_bond_refined_d0.026
r_gen_planes_refined0.011
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2411
Nucleic Acid Atoms
Solvent Atoms408
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing