6KZB

Transglutaminase2 complexed with calcium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PYG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	Potassium chloride, Magnesium acetate tetrahydrate, Sodium cacodylate, Polyethylene glycol 8000

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.08	α = 90
b = 216.307	β = 90
c = 166.263	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	125	CCD	ADSC QUANTUM 315r		2011-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	1.00000	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.55	42.585	99.99	0.113	8.95	10.9		29265

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.56	3.62			0.391

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4PYG	3.55	42.585	29242	1490	99.595	0.228	0.2266	0.2619	60.856

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]
0.016			-0.003		-0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.499
r_dihedral_angle_4_deg	19.17
r_dihedral_angle_3_deg	18.582
r_lrange_it	8.545
r_lrange_other	8.545
r_scangle_it	7.949
r_scangle_other	7.939
r_mcangle_it	6.724
r_mcangle_other	6.724
r_scbond_it	5.799
r_scbond_other	5.79
r_dihedral_angle_1_deg	4.603
r_mcbond_it	4.431
r_mcbond_other	4.431
r_angle_other_deg	2.311
r_angle_refined_deg	1.676
r_nbd_other	0.336
r_symmetry_xyhbond_nbd_refined	0.308
r_symmetry_nbd_other	0.26
r_symmetry_nbd_refined	0.251
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.208
r_xyhbond_nbd_other	0.193
r_nbtor_refined	0.189
r_symmetry_xyhbond_nbd_other	0.125
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.085
r_bond_other_d	0.036
r_gen_planes_other	0.029
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15665
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	90

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
Coot	model building