1XI3

Thiamine phosphate pyrophosphorylase from Pyrococcus furiosus Pfu-1255191-001

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G4T	pdb entry 1G4T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	modified microbatch	4.6	291	30%v/v PEG 2000 MME, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, modified microbatch, temperature 291KK

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.386	α = 90
b = 81.21	β = 90
c = 152.903	γ = 90

Symmetry
Space Group	I 2 2 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	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

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	1.7	30	100	0.098				50284

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)
	1.7	1.76	100		0.281

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-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 entry 1G4T	1.7	29.086	50281	1540	100	0.189	0.18878	0.188	0.2	0.2147	0.23	thin shells	16.981

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]
0.012			0.004		-0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.796
r_dihedral_angle_4_deg	13.605
r_dihedral_angle_3_deg	11.622
r_dihedral_angle_1_deg	5.348
r_scangle_it	4.355
r_mcangle_it	3.09
r_scbond_it	2.965
r_mcbond_it	2.603
r_mcangle_other	1.873
r_scangle_other	1.824
r_angle_refined_deg	1.367
r_scbond_other	0.889
r_angle_other_deg	0.831
r_mcbond_other	0.672
r_symmetry_vdw_refined	0.336
r_symmetry_vdw_other	0.311
r_nbd_refined	0.218
r_nbd_other	0.186
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.101
r_chiral_restr	0.081
r_nbtor_other	0.081
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3049
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	9

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
AMoRE	phasing