2X5Y

Human ZC3HAV1 (ARTD13), C-terminal domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PQFPDB ENTRY 2PQF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120 % PEG 3350, 0.2M NA-FLUORIDE
Crystal Properties
Matthews coefficientSolvent content
2.2345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.858α = 90
b = 54.103β = 90
c = 69.284γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2009-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.053595.20.0425.7780468
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)
11.051.0870.20.483.95.1

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 2PQF1.0531.847650440271000.13120.130260.14927RANDOM10.122
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]
0.220.08-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.749
r_dihedral_angle_4_deg23.845
r_dihedral_angle_3_deg11.723
r_dihedral_angle_1_deg6.594
r_scangle_it5.676
r_scbond_it3.967
r_mcangle_it3.102
r_mcbond_it2.02
r_angle_refined_deg1.934
r_rigid_bond_restr1.619
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.749
r_dihedral_angle_4_deg23.845
r_dihedral_angle_3_deg11.723
r_dihedral_angle_1_deg6.594
r_scangle_it5.676
r_scbond_it3.967
r_mcangle_it3.102
r_mcbond_it2.02
r_angle_refined_deg1.934
r_rigid_bond_restr1.619
r_angle_other_deg1.016
r_mcbond_other0.647
r_chiral_restr0.121
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1421
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing