3MAJ

Crystal structure of putative DNA processing protein DprA from Rhodopseudomonas palustris CGA009


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52970.1 M Tris-Cl, 1.5 M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.2344.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.215α = 90
b = 44.33β = 90
c = 75.81γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97937APS19-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
12.055099.60.07942.57.12336423262-335.3
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)
12.052.0999.60.6914.2371131

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.0543.772290322903118398.10.18690.18690.184440.23182RANDOM28.824
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]
-0.430.20.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.572
r_dihedral_angle_4_deg17.261
r_dihedral_angle_3_deg15.305
r_dihedral_angle_1_deg5.023
r_scangle_it3.952
r_scbond_it2.327
r_angle_refined_deg1.301
r_mcangle_it1.25
r_mcbond_it0.667
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.572
r_dihedral_angle_4_deg17.261
r_dihedral_angle_3_deg15.305
r_dihedral_angle_1_deg5.023
r_scangle_it3.952
r_scbond_it2.327
r_angle_refined_deg1.301
r_mcangle_it1.25
r_mcbond_it0.667
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2569
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms10

Software

Software
Software NamePurpose
SBC-Collectdata collection
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing