3B4M

Crystal Structure of Human PABPN1 RRM


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52830.1M HEPES, 4.2M sodium chloride, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
1.8934.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.338α = 90
b = 59.338β = 90
c = 80.599γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2007-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBSRF BEAMLINE 3W1A0.9800BSRF3W1A

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
12.81680.5820.0638.47694
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.8162.92

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3B4D2.8280.58733835499.880.229320.226310.2897RANDOM37.295
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]
1.10.551.1-1.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.991
r_dihedral_angle_4_deg23.039
r_dihedral_angle_3_deg17.844
r_dihedral_angle_1_deg5.966
r_scangle_it2.111
r_scbond_it1.394
r_angle_refined_deg1.252
r_mcangle_it0.989
r_mcbond_it0.65
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.991
r_dihedral_angle_4_deg23.039
r_dihedral_angle_3_deg17.844
r_dihedral_angle_1_deg5.966
r_scangle_it2.111
r_scbond_it1.394
r_angle_refined_deg1.252
r_mcangle_it0.989
r_mcbond_it0.65
r_nbtor_refined0.305
r_symmetry_hbond_refined0.27
r_nbd_refined0.208
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.173
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.004
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 Atoms2489
Nucleic Acid Atoms
Solvent Atoms33
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
AUTOMARdata reduction
MOLREPphasing