1VLP

Crystal structure of a putative nicotinate phosphoribosyltransferase (yor209c, npt1) from saccharomyces cerevisiae at 1.75 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	0.06M MES, 0.04M MES_Na, 14% PEG MME 5000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	15% PEG MME 5000, 0.06M MES, 0.04M MES_Na , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.9
2.29	45.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.406	α = 97.35
b = 83.103	β = 95.67
c = 107.237	γ = 97.99

Symmetry
Space Group	P 1

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		2004-01-08	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC		2003-12-19	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1
2	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0332, 0.9798	ALS	8.2.2

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
1,2	1.75	50	96.81	0.075	18.09	3.79		177740			28.97

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)
1,2	1.75	1.81	90.05		0.451	1.64	2.23	16630

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	MAD	THROUGHOUT	1.75	48.24	168817	8921	96.23	0.17163	0.16964	0.20962	RANDOM	7.224

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]
-0.03	0.01	-0.03	0.04	0.01	-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.483
r_dihedral_angle_4_deg	17.756
r_dihedral_angle_3_deg	13.068
r_scangle_it	6.54
r_dihedral_angle_1_deg	6.168
r_scbond_it	4.736
r_mcangle_it	2.854
r_mcbond_it	2.16
r_angle_refined_deg	1.544
r_angle_other_deg	0.859
r_mcbond_other	0.558
r_symmetry_vdw_refined	0.238
r_symmetry_vdw_other	0.235
r_nbd_refined	0.215
r_nbtor_refined	0.182
r_nbd_other	0.176
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.094
r_nbtor_other	0.085
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13317
Nucleic Acid Atoms
Solvent Atoms	1271
Heterogen Atoms	47

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXCD	phasing
SHARP	phasing
REFMAC	refinement
SHELXD	phasing