2AU3

Crystal Structure of the Aquifex aeolicus primase (Zinc Binding and RNA Polymerase Domains)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.529118-22% EtOH, 55 mM HEPES, 100 mM NaCl, pH 7.5, Microbatch, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1342

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.222α = 90
b = 66.403β = 90
c = 138.157γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102003-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.10.9792ALS8.3.1

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
1240990.07814.33.45274172598922
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)
122.0793.80.2863.33.22547

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 REPLACEMENTTHROUGHOUTLow-resolution Aquifex aeolicus DnaG from Tm-soak MAD2402598925989137798.930.204880.204880.203040.23826RANDOM26.19
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]
-1.631.9-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.75
r_scangle_it4.957
r_scbond_it2.886
r_mcangle_it2.055
r_angle_refined_deg1.223
r_mcbond_it1.155
r_nbd_refined0.214
r_symmetry_vdw_refined0.197
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.75
r_scangle_it4.957
r_scbond_it2.886
r_mcangle_it2.055
r_angle_refined_deg1.223
r_mcbond_it1.155
r_nbd_refined0.214
r_symmetry_vdw_refined0.197
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.149
r_chiral_restr0.103
r_metal_ion_refined0.068
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
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 Atoms3260
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing