3H25

Crystal structure of the catalytic domain of primase Repb' in complex with initiator DNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
150.2M AMMONIUM CITRATE, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
Crystal Properties
Matthews coefficientSolvent content
1.8834.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.35α = 90
b = 85.35β = 90
c = 68.89γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2007-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
12.71997.50.11116.517.2740072152
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)
12.72.77950.3945.647.3

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 REPLACEMENTTHROUGHOUTCATALYTIC DOMAIN OF PDB 3H20, MODEL OF IDEAL B-DNA2.71969973681000.2260.2240.274RANDOM31.47
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]
0.360.36-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.977
r_dihedral_angle_4_deg15.321
r_dihedral_angle_3_deg15.163
r_dihedral_angle_1_deg4.605
r_angle_refined_deg0.947
r_scangle_it0.658
r_mcangle_it0.353
r_scbond_it0.333
r_nbtor_refined0.28
r_mcbond_it0.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.977
r_dihedral_angle_4_deg15.321
r_dihedral_angle_3_deg15.163
r_dihedral_angle_1_deg4.605
r_angle_refined_deg0.947
r_scangle_it0.658
r_mcangle_it0.353
r_scbond_it0.333
r_nbtor_refined0.28
r_mcbond_it0.198
r_nbd_refined0.158
r_symmetry_vdw_refined0.125
r_xyhbond_nbd_refined0.106
r_symmetry_hbond_refined0.068
r_chiral_restr0.051
r_bond_refined_d0.005
r_gen_planes_refined0.002
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 Atoms1417
Nucleic Acid Atoms546
Solvent Atoms24
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling