4B2P

RadA C-terminal ATPase domain from Pyrococcus furiosus bound to GTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PZNPDB ENTRY 1PZN CHAIN A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.2pH 6.2
Crystal Properties
Matthews coefficientSolvent content
2.1442.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.32α = 90
b = 62.02β = 90
c = 87.17γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.636.5999.70.117.797.1293903
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)
11.61.798.30.823.067

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1PZN CHAIN A1.636.5927899149099.670.180680.17860.21976RANDOM15.96
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]
0.080.26-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.606
r_dihedral_angle_4_deg14.682
r_dihedral_angle_3_deg13.019
r_scangle_it6.287
r_dihedral_angle_1_deg5.569
r_scbond_it3.936
r_mcangle_it2.418
r_angle_refined_deg2.153
r_mcbond_it1.418
r_chiral_restr0.178
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.606
r_dihedral_angle_4_deg14.682
r_dihedral_angle_3_deg13.019
r_scangle_it6.287
r_dihedral_angle_1_deg5.569
r_scbond_it3.936
r_mcangle_it2.418
r_angle_refined_deg2.153
r_mcbond_it1.418
r_chiral_restr0.178
r_bond_refined_d0.026
r_gen_planes_refined0.011
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1646
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing