2HXV | pdb_00002hxv

Crystal structure of a diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5-amino-6-(5-phosphoribosylamino)uracil reductase (tm1828) from thermotoga maritima at 1.80 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	7.5	277	5.0% PEG-3000, 10.0% Glycerol, 30.0% PEG-400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP, NANODROP	7.5	277	5.0% PEG-3000, 10.0% Glycerol, 30.0% PEG-400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.18	α = 90
b = 104.18	β = 90
c = 145.89	γ = 90

Symmetry
Space Group	I 4 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	ADSC QUANTUM 315	Flat mirror (vertical focusing)	2006-07-17	M	MAD
2	2

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	1.000001	SSRL	BL11-1
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979170, 0.918370, 0.978913	SSRL	BL11-1

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	1.8	28.341	99.7	0.072	14.96	4.945		37367			30.526

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	1.8	1.86	97.7		0.719	1.71	3.711	5938

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.8	28.341	37365	1877	99.84	0.162	0.16	0.17	0.195	0.2	RANDOM	28.964

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]
0.46			0.46		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.676
r_dihedral_angle_4_deg	14.474
r_dihedral_angle_3_deg	12.044
r_scangle_it	7.869
r_dihedral_angle_1_deg	5.695
r_scbond_it	5.473
r_mcangle_it	3.353
r_mcbond_it	2.415
r_angle_refined_deg	1.69
r_angle_other_deg	0.999
r_mcbond_other	0.641
r_symmetry_vdw_other	0.257
r_nbd_refined	0.209
r_nbd_other	0.19
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.188
r_symmetry_hbond_refined	0.177
r_symmetry_vdw_refined	0.148
r_chiral_restr	0.099
r_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2697
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	98

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	phasing