3C2O

Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Sachharomyces cerevisiae complexed with quinolinate

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	20% PEG 3000, 0.1 M citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.802	α = 90
b = 154.802	β = 90
c = 68.621	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARMOSAIC 225 mm CCD		2005-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.88557	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	30	100	0.094	0.094	16.7	11.1	14088	14088	1	1	36.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.36	100		0.396	0.396	5.4	10.8	1029

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.3	29.26	13774	559	97.8	0.207	0.206	0.237	RANDOM	36.601

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]
-3.24	-1.62		-3.24		4.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.293
r_dihedral_angle_4_deg	23.69
r_scangle_it	18.087
r_scbond_it	15.389
r_dihedral_angle_3_deg	14.959
r_mcangle_it	11.305
r_mcbond_it	9.583
r_dihedral_angle_1_deg	9.025
r_angle_other_deg	4.309
r_mcbond_other	3.606
r_angle_refined_deg	1.756
r_xyhbond_nbd_refined	0.352
r_symmetry_hbond_refined	0.315
r_symmetry_vdw_other	0.298
r_nbd_other	0.297
r_nbd_refined	0.26
r_symmetry_vdw_refined	0.216
r_nbtor_refined	0.198
r_chiral_restr	0.165
r_nbtor_other	0.12
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2023
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	12

Software

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