3C2V | pdb_00003c2v

Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP and 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 ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.668	α = 90
b = 154.668	β = 90
c = 69.346	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	BRUKER SMART 2000		2005-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR-H	1.5418

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	50	99.2	0.083	0.083	3.95	4.6	14205	14089	1	1	50.6

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	2.38	98.4		0.39	0.39	3.95	4	1388

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	2.29	44.63	12818	514	90.99	0.227	0.225	0.23	0.282	0.3	RANDOM	50.579

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]
-5.24	-2.62		-5.24		7.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.358
r_dihedral_angle_4_deg	19.919
r_dihedral_angle_3_deg	15.1
r_dihedral_angle_1_deg	12.026
r_scangle_it	3.093
r_scbond_it	2.131
r_mcangle_it	1.704
r_angle_refined_deg	1.675
r_mcbond_it	0.983
r_chiral_restr	0.578

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.358
r_dihedral_angle_4_deg	19.919
r_dihedral_angle_3_deg	15.1
r_dihedral_angle_1_deg	12.026
r_scangle_it	3.093
r_scbond_it	2.131
r_mcangle_it	1.704
r_angle_refined_deg	1.675
r_mcbond_it	0.983
r_chiral_restr	0.578
r_nbtor_refined	0.336
r_nbd_refined	0.313
r_symmetry_hbond_refined	0.282
r_symmetry_vdw_refined	0.268
r_xyhbond_nbd_refined	0.196
r_bond_refined_d	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2067
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	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.