2GA1

Crystal structure of a duf433 member protein (ava_0674) from anabaena variabilis atcc 29413 at 2.00 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP6.527720.0% Glycerol, 0.16M Mg(oAc)2, 16.0% PEG-8000, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.850.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.98α = 90
b = 65.12β = 90
c = 86.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3151m long Rh coated bent cylindrical mirror for horizontal and vertical focusing2006-02-14MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL1-50.918381, 0.978489, 0.979094SSRLBL1-5

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
1228.6499.10.0568.863.5491853532.644
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)
122.0797.30.3422.33

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT228.641849195899.320.1780.1760.218RANDOM29.739
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]
2.03-0.7-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.498
r_dihedral_angle_4_deg16.942
r_dihedral_angle_3_deg12.846
r_scangle_it6.748
r_scbond_it5.097
r_dihedral_angle_1_deg4.889
r_mcangle_it2.995
r_mcbond_it2.256
r_angle_refined_deg1.485
r_angle_other_deg0.852
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.498
r_dihedral_angle_4_deg16.942
r_dihedral_angle_3_deg12.846
r_scangle_it6.748
r_scbond_it5.097
r_dihedral_angle_1_deg4.889
r_mcangle_it2.995
r_mcbond_it2.256
r_angle_refined_deg1.485
r_angle_other_deg0.852
r_mcbond_other0.533
r_nbd_refined0.218
r_symmetry_vdw_refined0.207
r_symmetry_vdw_other0.191
r_symmetry_hbond_refined0.19
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.175
r_nbd_other0.168
r_chiral_restr0.086
r_nbtor_other0.085
r_bond_refined_d0.018
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1588
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SOLVEphasing