1RKS

E. COLI RIBOKINASE IN COMPLEX WITH D-RIBOSE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.45 MM RIBOSE, 10 MM MGCL2 IN THE DROP, 0.1 M TRIS-HCL BUFFER, PH 8.4 WITH 2.1-2.4 M NH4H2PO4 AS PRECIPITANT, VAPOR DIFFUSION, HANGING DROP CRYO-SOLUTION: MOTHER LIQUOR CONTAINING 20% GLYCEROL. SOAK-TIME: 2-3 MINUTES.
Crystal Properties
Matthews coefficientSolvent content
3.148.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.21α = 90
b = 95.21β = 90
c = 154.46γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IIMSC MIRRORS1997-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.42999.90.06930.210.51681440
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)
12.42.4499.80.3545.87.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONOTHERTHROUGHOUT2.41516740166899.90.2310.2290.288RANDOM45.3
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor31.2
p_staggered_tor14
p_scangle_it3.982
p_planar_tor3.9
p_scbond_it2.876
p_mcangle_it1.342
p_mcbond_it0.753
p_multtor_nbd0.26
p_singtor_nbd0.188
p_xyhbond_nbd0.167
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor31.2
p_staggered_tor14
p_scangle_it3.982
p_planar_tor3.9
p_scbond_it2.876
p_mcangle_it1.342
p_mcbond_it0.753
p_multtor_nbd0.26
p_singtor_nbd0.188
p_xyhbond_nbd0.167
p_chiral_restr0.113
p_planar_d0.036
p_angle_d0.032
p_plane_restr0.021
p_bond_d0.011
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2236
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling