3GLL

Crystal structure of Polynucleotide Phosphorylase (PNPase) core


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.2 M ammonium nitrate, 20 % w/v PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2261.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.153α = 90
b = 159.153β = 90
c = 157.508γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMonochromator2006-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

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
12.72096.70.1259.22.9205221941422
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)
2.72.7696.70.4321.82.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.719.392052219414105396.810.272450.270750.30572RANDOM48.035
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]
0.060.030.06-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.129
r_dihedral_angle_3_deg13.007
r_dihedral_angle_4_deg10.4
r_scangle_it6.87
r_dihedral_angle_1_deg4.896
r_scbond_it4.363
r_mcangle_it3.731
r_mcbond_it2.791
r_angle_refined_deg0.746
r_symmetry_vdw_refined0.585
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.129
r_dihedral_angle_3_deg13.007
r_dihedral_angle_4_deg10.4
r_scangle_it6.87
r_dihedral_angle_1_deg4.896
r_scbond_it4.363
r_mcangle_it3.731
r_mcbond_it2.791
r_angle_refined_deg0.746
r_symmetry_vdw_refined0.585
r_chiral_restr0.295
r_nbtor_refined0.289
r_nbd_refined0.171
r_xyhbond_nbd_refined0.161
r_symmetry_hbond_refined0.048
r_bond_refined_d0.006
r_gen_planes_refined0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3630
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement