1T9H | pdb_00001t9h

The crystal structure of YloQ, a circularly permuted GTPase.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291PEG 5000, calcium acetate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.346.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.97α = 90
b = 47.97β = 90
c = 279.89γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 4Si mirror2003-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.870SRSPX9.6

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
11.62299.40.1276.34.74462644626
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)
1.61.6699.70.52.74.34339

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUT1.620.5422114221122431000.145650.145650.143960.210.178010.23RANDOM22.801
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]
-0.05-0.050.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.762
r_dihedral_angle_4_deg16.364
r_dihedral_angle_3_deg14.64
r_dihedral_angle_1_deg6.111
r_scangle_it4.568
r_sphericity_free4.347
r_scbond_it3.398
r_mcangle_it3.18
r_mcbond_it2.345
r_rigid_bond_restr2.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.762
r_dihedral_angle_4_deg16.364
r_dihedral_angle_3_deg14.64
r_dihedral_angle_1_deg6.111
r_scangle_it4.568
r_sphericity_free4.347
r_scbond_it3.398
r_mcangle_it3.18
r_mcbond_it2.345
r_rigid_bond_restr2.063
r_sphericity_bonded1.952
r_angle_refined_deg1.253
r_angle_other_deg0.967
r_mcbond_other0.966
r_metal_ion_refined0.338
r_symmetry_hbond_refined0.268
r_symmetry_vdw_other0.256
r_nbd_refined0.224
r_xyhbond_nbd_refined0.223
r_symmetry_vdw_refined0.221
r_nbd_other0.187
r_nbtor_other0.081
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2322
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing