2GM8

TenA Homolog/Thi-4 Thiaminase complexed with product 4-amino-5-hydroxymethyl-2-methylpyrimidine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	18 mg/mL protein was complexed with thiamine diphosphate and enzyme mediated catalysis produced 4-amino-5-hydroxymethyl-2-methylpyrimidine. Reservoir contains 20% PEG 8000, 0.1M Tris pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.647	α = 90
b = 94.287	β = 113.65
c = 73.198	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	CCD	ADSC QUANTUM 315		2005-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00000	ALS	5.0.2

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	2.5	80	99	0.11	13	2.9	32375	32375			53

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	2.5	2.59	98.3	98.3	0.299		2.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 2GM7	2.5	67.12	30264	30264	1533	99.08	0.189	0.189	0.187	0.237	RANDOM	29.708

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]
2.28		1.05	-2.57		1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.007
r_dihedral_angle_4_deg	21.95
r_dihedral_angle_3_deg	17.166
r_scangle_it	10.862
r_scbond_it	9.301
r_mcangle_it	8.085
r_mcbond_it	7.35
r_dihedral_angle_1_deg	3.453
r_mcbond_other	1.962
r_angle_refined_deg	1.308
r_angle_other_deg	0.895
r_xyhbond_nbd_other	0.254
r_nbd_refined	0.246
r_symmetry_vdw_other	0.218
r_nbtor_refined	0.21
r_nbd_other	0.206
r_xyhbond_nbd_refined	0.173
r_symmetry_vdw_refined	0.122
r_chiral_restr	0.104
r_nbtor_other	0.096
r_symmetry_hbond_refined	0.092
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6920
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	48

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection