3B7G | pdb_00003b7g

Human DEAD-box RNA helicase DDX20, Conserved domain I (DEAD) in complex with AMPPNP (Adenosine-(Beta,gamma)-imidotriphosphate)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OXCPDB entry 2OXC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.527725% PEG 3350, 200mM Ammonium acetate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4950.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.56α = 90
b = 63.56β = 90
c = 214.6γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2007-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.00595ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.94599.70.0810.02332.120.54064240642
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921000.1260.04121.318.25705

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 2OXC1.938.43386063860620321000.173680.173680.172190.180.202190.21RANDOM14.938
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]
-0.08-0.04-0.080.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.981
r_dihedral_angle_4_deg18.811
r_dihedral_angle_3_deg12.681
r_dihedral_angle_1_deg5.321
r_scangle_it3.273
r_scbond_it2.405
r_angle_refined_deg1.648
r_mcangle_it1.273
r_mcbond_it1.087
r_angle_other_deg0.995
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.981
r_dihedral_angle_4_deg18.811
r_dihedral_angle_3_deg12.681
r_dihedral_angle_1_deg5.321
r_scangle_it3.273
r_scbond_it2.405
r_angle_refined_deg1.648
r_mcangle_it1.273
r_mcbond_it1.087
r_angle_other_deg0.995
r_symmetry_hbond_refined0.497
r_symmetry_vdw_other0.352
r_mcbond_other0.262
r_nbd_refined0.212
r_nbd_other0.193
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.153
r_symmetry_vdw_refined0.089
r_chiral_restr0.084
r_nbtor_other0.084
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3156
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing