2XZZ | pdb_00002xzz

Crystal structure of the human transglutaminase 1 beta-barrel domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FIE	PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE
experimental model	PDB	1GGY	PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE
experimental model	PDB	1G0D	PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE
experimental model	PDB	1QRK	PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.7 M (NH4)2SO4, 1% PEG3350, 0.1 M BIS-TRIS (PH 5.5)

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.74	α = 90
b = 115.74	β = 90
c = 115.74	γ = 90

Symmetry
Space Group	I 4 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD		2010-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	19.29	99.6	0.07	21	10.8		6155		2	54.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	100		0.63	4.1	11.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE	2.3	19.29	5852	290	99.59	0.22118	0.21901	0.21	0.26688	0.26	RANDOM	42.281

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.497
r_dihedral_angle_3_deg	17.202
r_dihedral_angle_4_deg	12.862
r_scangle_it	7.705
r_dihedral_angle_1_deg	6.096
r_scbond_it	5.147
r_mcangle_it	3.587
r_mcbond_it	2.002
r_angle_refined_deg	1.829
r_angle_other_deg	0.951
r_mcbond_other	0.454
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	705
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing