3C2R | pdb_00003c2r

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	20% PEG 3350, 0.2 M potassium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.524	α = 90
b = 155.524	β = 90
c = 121.072	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		CCD	MARMOSAIC 325 mm CCD		2005-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	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	2.4	46.932	100	0.099	0.099	6.4	10.9	22088	22088	1	1	50

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)
	2.4	2.46	100		0.578	0.578	1.3	11	1622

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.4	46.93	21560	2189	97.62	0.188	0.183	0.22	0.225	0.25	RANDOM	50.701

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]
-1.28	-0.64		-1.28		1.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.526
r_scangle_it	25.389
r_scbond_it	24.872
r_dihedral_angle_4_deg	21.9
r_dihedral_angle_3_deg	18.412
r_mcangle_it	17.27
r_mcbond_it	15.399
r_dihedral_angle_1_deg	2.079
r_angle_refined_deg	1.937
r_nbtor_refined	0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.526
r_scangle_it	25.389
r_scbond_it	24.872
r_dihedral_angle_4_deg	21.9
r_dihedral_angle_3_deg	18.412
r_mcangle_it	17.27
r_mcbond_it	15.399
r_dihedral_angle_1_deg	2.079
r_angle_refined_deg	1.937
r_nbtor_refined	0.34
r_nbd_refined	0.306
r_symmetry_vdw_refined	0.279
r_xyhbond_nbd_refined	0.205
r_symmetry_hbond_refined	0.181
r_chiral_restr	0.123
r_bond_refined_d	0.018
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4082
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	24

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.