3C2E | pdb_00003c2e

Crystal structure at 1.9A of the apo quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	20% PEG 3350, 0.2 M ammonium formate; holo-quinolinate: 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 = 154.913	α = 90
b = 154.913	β = 90
c = 68.946	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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979126	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	1.9	30	94.9	0.064	0.064	17.8	9	25007	23727	1	1	44.4

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)
	1.9	1.97	72.5		0.31	0.31	2.98	4.9	1810

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	1.9	28.1	2	21799	1109	91.87	0.235	0.234	0.24	0.259	0.26	RANDOM	44.407

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]
-2.82	-1.41		-2.82		4.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.556
r_dihedral_angle_4_deg	22.57
r_scangle_it	18.712
r_dihedral_angle_3_deg	15.839
r_scbond_it	15.171
r_mcangle_it	10.494
r_mcbond_it	8.803
r_dihedral_angle_1_deg	1.306
r_angle_refined_deg	1.288
r_symmetry_hbond_refined	0.354

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.556
r_dihedral_angle_4_deg	22.57
r_scangle_it	18.712
r_dihedral_angle_3_deg	15.839
r_scbond_it	15.171
r_mcangle_it	10.494
r_mcbond_it	8.803
r_dihedral_angle_1_deg	1.306
r_angle_refined_deg	1.288
r_symmetry_hbond_refined	0.354
r_nbtor_refined	0.326
r_symmetry_vdw_refined	0.285
r_nbd_refined	0.284
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.097
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2042
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.