3DKP

Human DEAD-box RNA-helicase DDX52, conserved domain I in complex with ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DB3PDB entry 2DB3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP827710% PEG 8000, 100 mM Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.141.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.63α = 90
b = 38.36β = 90.37
c = 73.84γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2008-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.00000ESRFID23-1

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
12.12099.50.08812.83.65134801348025.8
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)
12.12.299.80.3784.613.681731

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2DB32.119.56128041280467499.620.184510.184510.181660.20.236360.25RANDOM9.348
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]
0.680.060.13-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.382
r_dihedral_angle_4_deg15.803
r_dihedral_angle_3_deg14.985
r_dihedral_angle_1_deg5.911
r_scangle_it3.258
r_scbond_it1.976
r_angle_refined_deg1.414
r_mcangle_it1.19
r_mcbond_it0.624
r_chiral_restr0.097
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1868
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing