1RKD

E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.4CRYSTALS WERE GROWN IN THE PRESENCE OF 0.5 MM RIBOSE, 10 MM AMP-PNP AND 10 MM MGCL2 USING 2.1-2.4 M NH4H2PO4 AS PRECIPITANT AND BUFFERED TO PH 8.4 WITH 0.1 M TRIS-HCL.
Crystal Properties
Matthews coefficientSolvent content
3.149

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.4α = 90
b = 95.4β = 90
c = 154.87γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90IMAGE PLATEMARRESEARCH1996-11-16M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
11.843095.50.05530.27.53501523
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)
11.841.8797.80.2397.47.5

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 DIFFRACTIONMULTIPLE ISOMORPHOUS REPLACEMENTTHROUGHOUT1.842835013354295.50.2210.220.258RANDOM29
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_tor29.6
p_staggered_tor16.2
p_scangle_it5
p_planar_tor4.2
p_scbond_it3.5
p_mcangle_it2
p_mcbond_it1.4
p_multtor_nbd0.25
p_singtor_nbd0.18
p_xyhbond_nbd0.15
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor29.6
p_staggered_tor16.2
p_scangle_it5
p_planar_tor4.2
p_scbond_it3.5
p_mcangle_it2
p_mcbond_it1.4
p_multtor_nbd0.25
p_singtor_nbd0.18
p_xyhbond_nbd0.15
p_chiral_restr0.13
p_planar_d0.033
p_angle_d0.028
p_plane_restr0.02
p_bond_d0.013
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 Atoms2248
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms47

Software

Software
Software NamePurpose
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling