4P8E

Structure of ribB complexed with substrate (Ru5P) and metal ions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G58 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.1293PEG3350, Na2HPO4
Crystal Properties
Matthews coefficientSolvent content
2.0840.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.079α = 90
b = 77.09β = 90
c = 97.531γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMirror2010-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.042098.30.06523.17.325330-321
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)
12.042.1692.70.2586.46.1

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 REPLACEMENTTHROUGHOUT1G582.042024042128798.50.178440.17560.23216RANDOM22.487
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]
-1.131.97-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.823
r_dihedral_angle_4_deg14.013
r_dihedral_angle_3_deg13.17
r_dihedral_angle_1_deg5.288
r_long_range_B_refined3.575
r_long_range_B_other3.574
r_scangle_other1.742
r_mcangle_it1.366
r_mcangle_other1.366
r_angle_refined_deg1.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.823
r_dihedral_angle_4_deg14.013
r_dihedral_angle_3_deg13.17
r_dihedral_angle_1_deg5.288
r_long_range_B_refined3.575
r_long_range_B_other3.574
r_scangle_other1.742
r_mcangle_it1.366
r_mcangle_other1.366
r_angle_refined_deg1.147
r_scbond_it1.047
r_scbond_other1.047
r_mcbond_it0.831
r_mcbond_other0.826
r_angle_other_deg0.721
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3265
Nucleic Acid Atoms
Solvent Atoms277
Heterogen Atoms70

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
PHASERphasing