1O5O | pdb_00001o5o

Crystal structure of Uracil phosphoribosyltransferase (TM0721) from Thermotoga maritima at 2.30 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I5E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	9	277	2.4M ammonium sulfate, 0.1M bicine pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.078	α = 90
b = 87.406	β = 115.29
c = 90.826	γ = 90

Symmetry
Space Group	C 1 2 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 4	bent conical Si-mirror (Rh coating)	2003-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C

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	2.3	50	100	0.102	10.16	3.72	41796	41796			51.25

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	2.3	2.38	99.71		0.752	1.49	3.66	4138

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 (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	1i5e	2.3	30.93	39885	2126	99.68	0.17004	0.16658	0.18	0.23635	0.24	RANDOM	45.165

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]
-0.39		-0.13	0.53		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.392
r_dihedral_angle_4_deg	17.785
r_dihedral_angle_3_deg	17.403
r_dihedral_angle_1_deg	6.566
r_scangle_it	3.466
r_scbond_it	2.216
r_angle_refined_deg	1.702
r_mcangle_it	1.39
r_mcbond_it	0.966
r_angle_other_deg	0.915
r_symmetry_hbond_refined	0.196
r_nbd_refined	0.19
r_nbd_other	0.188
r_xyhbond_nbd_refined	0.184
r_symmetry_vdw_refined	0.175
r_symmetry_vdw_other	0.17
r_chiral_restr	0.096
r_nbtor_other	0.091
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6554
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	129

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement