7POH

Crystal structure of ZAD-domain of Serendipity-d protein from D.melanogaster


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52880.1M HEPES pH 7.5, 1.3M Lithium sulfate 1.3M, 0.1M Sodium chloride

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.161α = 90
b = 99.161β = 90
c = 117.667γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.8599.1691.30.0890.10.0450.99494.512833
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.85392.90.8530.9610.4310.6494.7

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 DIFFRACTIONSADTHROUGHOUT2.8570.121218363389.80.21870.21760.2404RANDOM79.734
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]
0.960.96-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.638
r_dihedral_angle_4_deg20.888
r_dihedral_angle_3_deg19.672
r_dihedral_angle_1_deg11.445
r_angle_refined_deg2.542
r_angle_other_deg1.427
r_chiral_restr0.122
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.638
r_dihedral_angle_4_deg20.888
r_dihedral_angle_3_deg19.672
r_dihedral_angle_1_deg11.445
r_angle_refined_deg2.542
r_angle_other_deg1.427
r_chiral_restr0.122
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.004
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1376
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
SHELXphasing
PDB_EXTRACTdata extraction