Experiment: 1NUD

Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 calciums, active form)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L9N	PDB Entry 1L9N

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
2.62	53.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.54	α = 90
b = 115.37	β = 92.66
c = 121.39	γ = 90

Symmetry
Space Group	P 1 21 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	2000-06-07	M	SINGLE WAVELENGTH
2	1		CCD	ADSC QUANTUM 4	mirrors	2000-06-07

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	2.7	20	93.7	8.9		41052	41052	2	2	23.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.87	88.4

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-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry 1L9N	2.7	20	41052	39296	3958		0.199	0.265	RANDOM	21.6

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]
-4.67		0.83	1.08		3.6

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.5
c_angle_d	1.3
c_mcangle_it	0.87
c_scangle_it	0.86
c_improper_angle_d	0.76
c_scbond_it	0.52
c_mcbond_it	0.47
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10500
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms	23

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction