4P77

Structure of ribB complexed with substrate Ru5P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4P6D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.1293Na2HPO4, PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.0539.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.408α = 90
b = 74.086β = 90
c = 99.331γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMIRROR2010-06-25MSINGLE 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
12.042099.40.08519.26.926194-324.43
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)
12.042.1697.80.5353.76.6

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 REPLACEMENTTHROUGHOUT4P6D2.042024866132899.390.175890.173380.22356RANDOM29.592
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]
2.23-1.05-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.451
r_dihedral_angle_3_deg13.754
r_dihedral_angle_4_deg13.463
r_dihedral_angle_1_deg5.782
r_long_range_B_refined5.155
r_long_range_B_other5.155
r_scangle_other3.07
r_mcangle_it2.261
r_mcangle_other2.261
r_scbond_it1.898
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.451
r_dihedral_angle_3_deg13.754
r_dihedral_angle_4_deg13.463
r_dihedral_angle_1_deg5.782
r_long_range_B_refined5.155
r_long_range_B_other5.155
r_scangle_other3.07
r_mcangle_it2.261
r_mcangle_other2.261
r_scbond_it1.898
r_scbond_other1.896
r_mcbond_it1.455
r_mcbond_other1.454
r_angle_refined_deg1.31
r_angle_other_deg0.752
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms3196
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing