6A4F

Separated uridine bound Oligoribonuclease (ORN) from Colwellia psychrerythraea strain 34H


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M potassium thiocyanate, 20% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.8456.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.285α = 90
b = 59.285β = 90
c = 234.16γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 315r2017-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.9796PAL/PLS5C (4A)

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
12.215086.243.94.821675
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.212.25

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 DIFFRACTIONTHROUGHOUT2.2147.0220644103186.350.196740.193040.27018RANDOM57.033
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]
0.020.010.02-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.917
r_dihedral_angle_4_deg25.772
r_dihedral_angle_3_deg17.715
r_long_range_B_refined9.416
r_long_range_B_other9.397
r_dihedral_angle_1_deg7.796
r_scangle_other7.359
r_mcangle_it6.716
r_mcangle_other6.716
r_scbond_it5.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.917
r_dihedral_angle_4_deg25.772
r_dihedral_angle_3_deg17.715
r_long_range_B_refined9.416
r_long_range_B_other9.397
r_dihedral_angle_1_deg7.796
r_scangle_other7.359
r_mcangle_it6.716
r_mcangle_other6.716
r_scbond_it5.288
r_scbond_other5.285
r_mcbond_it4.933
r_mcbond_other4.93
r_angle_refined_deg1.884
r_angle_other_deg1.052
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2930
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
MxDCdata collection
HKL-2000data scaling