2XZZ | pdb_00002xzz

Crystal structure of the human transglutaminase 1 beta-barrel domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FIEPDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE
experimental modelPDB 1GGYPDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE
experimental modelPDB 1G0DPDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE
experimental modelPDB 1QRKPDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.7 M (NH4)2SO4, 1% PEG3350, 0.1 M BIS-TRIS (PH 5.5)
Crystal Properties
Matthews coefficientSolvent content
2.8757.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.74α = 90
b = 115.74β = 90
c = 115.74γ = 90
Symmetry
Space GroupI 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
12.319.2999.60.072110.86155254.4
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)
12.32.421000.634.111.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE2.319.29585229099.590.221180.219010.210.266880.26RANDOM42.281
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.497
r_dihedral_angle_3_deg17.202
r_dihedral_angle_4_deg12.862
r_scangle_it7.705
r_dihedral_angle_1_deg6.096
r_scbond_it5.147
r_mcangle_it3.587
r_mcbond_it2.002
r_angle_refined_deg1.829
r_angle_other_deg0.951
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms705
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing