1ZAO

Crystal Structure of A.fulgidus Rio2 Kinase Complexed With ATP and Manganese Ions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TQIPDB entry 1TQI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.78293PEG 900, SODIUM PHOSPHATE, SODIUM CITRATE , pH 3.78, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5851.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.862α = 90
b = 44.365β = 94.01
c = 62.793γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.99997APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8463.250.0353.92817527131
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.841.88768.20.1143.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1TQI1.8463.252676527131136196.250.18350.18350.2124RANDOM25.191
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]
-0.480.84-0.471.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.587
r_dihedral_angle_4_deg18.955
r_dihedral_angle_3_deg14.071
r_dihedral_angle_1_deg5.713
r_scangle_it4.53
r_scbond_it2.892
r_mcangle_it1.753
r_angle_refined_deg1.414
r_mcbond_it1.159
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.587
r_dihedral_angle_4_deg18.955
r_dihedral_angle_3_deg14.071
r_dihedral_angle_1_deg5.713
r_scangle_it4.53
r_scbond_it2.892
r_mcangle_it1.753
r_angle_refined_deg1.414
r_mcbond_it1.159
r_nbtor_refined0.307
r_nbd_refined0.202
r_symmetry_vdw_refined0.199
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.149
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.006
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 Atoms2204
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing