2BX2

Catalytic domain of E. coli RNase E


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18CRYSTALS OF THE RNASE E CATALYTIC DOMAIN/ RNA COMPLEX APPEARED AFTER TWO TO FOUR WEEKS IN 5 TO 20 % WT/V POLYETHYLENE GLYCOL 8,000, 0.1 M TRIS PH 7.5 TO 8.0, AND 10 TO 50 MM MAGNESIUM FORMATE AT 20OC
Crystal Properties
Matthews coefficientSolvent content
6.682

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 195.838α = 90
b = 195.838β = 90
c = 143.569γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.92597.40.117.99.2361332
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)
12.85396.70.813.59

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 DIFFRACTIONMADTHROUGHOUT2.852536133190399.50.2310.230.257RANDOM56.15
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]
0.350.170.35-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.458
r_dihedral_angle_3_deg17.863
r_dihedral_angle_4_deg15.722
r_dihedral_angle_1_deg7.445
r_scangle_it2.889
r_mcangle_it2.531
r_scbond_it1.711
r_angle_refined_deg1.551
r_mcbond_it1.5
r_nbtor_refined0.345
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.458
r_dihedral_angle_3_deg17.863
r_dihedral_angle_4_deg15.722
r_dihedral_angle_1_deg7.445
r_scangle_it2.889
r_mcangle_it2.531
r_scbond_it1.711
r_angle_refined_deg1.551
r_mcbond_it1.5
r_nbtor_refined0.345
r_symmetry_vdw_refined0.335
r_nbd_refined0.317
r_xyhbond_nbd_refined0.296
r_symmetry_hbond_refined0.224
r_chiral_restr0.117
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3783
Nucleic Acid Atoms293
Solvent Atoms56
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling