1L9M | pdb_00001l9m

Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions change structure for activation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GGT	PDB ENTRY 1GGT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	288	4%(W/V) Peg 20K, 100 mM Tris_HCl(pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.709	α = 97.24
b = 67.515	β = 90.15
c = 116.208	γ = 98.67

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IIC	mirrors	1999-08-15	M	SINGLE WAVELENGTH
2	1		CCD	ADSC QUANTUM 4	mirrors	2000-07-26

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418
2	SYNCHROTRON	NSLS BEAMLINE X9B	0.92	NSLS	X9B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	20	93	11.3			75013		-3	15.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	20	93

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1GGT	2.1	20	72799	72799	7350		0.248	0.296	0.182	0.225	RANDOM	26.3

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]
-3.03	-2.78	-0.56	6.12	1.32	-3.09

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.54
c_scangle_it	1.79
c_mcangle_it	1.48
c_angle_deg	1.24
c_scbond_it	1.19
c_mcbond_it	0.86
c_improper_angle_d	0.74
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10580
Nucleic Acid Atoms
Solvent Atoms	901
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.