3D45

Crystal structure of mouse PARN in complex with m7GpppG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A1R2A1R 1WHV
experimental modelPDB 1WHV2A1R 1WHV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62936~10% PEG6000, 100mM MES, pH6.0, 10mM betaine , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8256.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.013α = 90
b = 128.35β = 90
c = 176.844γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9793ESRFBM14

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
13103.69960.1016.92959229592
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)
133.1960.3272.35.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2A1R 1WHV3103.6924512129394.660.300350.29860.33371RANDOM76.434
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]
4.62-2.58-2.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.074
r_dihedral_angle_3_deg21.156
r_dihedral_angle_4_deg15.684
r_dihedral_angle_1_deg6.511
r_scangle_it1.826
r_angle_refined_deg1.532
r_mcangle_it1.183
r_scbond_it1.129
r_mcbond_it0.649
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.074
r_dihedral_angle_3_deg21.156
r_dihedral_angle_4_deg15.684
r_dihedral_angle_1_deg6.511
r_scangle_it1.826
r_angle_refined_deg1.532
r_mcangle_it1.183
r_scbond_it1.129
r_mcbond_it0.649
r_nbtor_refined0.323
r_symmetry_vdw_refined0.265
r_nbd_refined0.256
r_symmetry_hbond_refined0.205
r_xyhbond_nbd_refined0.197
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6125
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing