3GCM

Crystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293.150.2 M ammonium hydrogen citrate, 17 % w/v PEG 3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
3.8467.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.335α = 90
b = 176.335β = 90
c = 189.628γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDMARMOSAIC 225 mm CCDMonochromator2006-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.52099.36.6102846976452227.176
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)
2.52.5999.50.6192.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1E3H2.52010284697645513499.360.2010.169110.166390.22065RANDOM27.176
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
r_dihedral_angle_2_deg39.495
r_dihedral_angle_4_deg20.703
r_dihedral_angle_3_deg15.951
r_dihedral_angle_1_deg6.735
r_scangle_it5.44
r_scbond_it3.361
r_mcangle_it2.01
r_angle_refined_deg1.939
r_angle_other_deg1.247
r_mcbond_it1.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.495
r_dihedral_angle_4_deg20.703
r_dihedral_angle_3_deg15.951
r_dihedral_angle_1_deg6.735
r_scangle_it5.44
r_scbond_it3.361
r_mcangle_it2.01
r_angle_refined_deg1.939
r_angle_other_deg1.247
r_mcbond_it1.229
r_nbtor_refined0.309
r_nbd_refined0.228
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.161
r_symmetry_hbond_refined0.159
r_chiral_restr0.152
r_nbd_other0.14
r_nbtor_other0.051
r_bond_refined_d0.022
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12865
Nucleic Acid Atoms
Solvent Atoms884
Heterogen Atoms167

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling