2H0R | pdb_00002h0r

Structure of the Yeast Nicotinamidase Pnc1p

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	298	0.9M sodium citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
5.62	78.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 302.04	α = 90
b = 302.04	β = 90
c = 112.12	γ = 120

Symmetry
Space Group	H 3

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	CUSTOM-MADE		2004-02-11	M	SINGLE WAVELENGTH
2	1		CCD	CUSTOM-MADE		2004-08-19
3	1		CCD	ADSC QUANTUM 210		2004-11-23
4	1		CCD	ADSC QUANTUM 210		2004-11-23

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	1.0332	APS	19-BM
2	SYNCHROTRON	APS BEAMLINE 19-BM	1.0719	APS	19-BM
3	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.1401,1.1405,1.1390	ALS	8.2.1
4	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.8000	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.9	50	100	0.07	21	4.4	84498	84498			71.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	100		0.559	3.4	4.3	8439

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD+MIRAS	THROUGHOUT	2.9	50	80251	80251	4226	99.95	0.19066	0.19066	0.18912	0.19	0.21997	0.22	RANDOM	77.431

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]
0.7	0.35		0.7		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.6
r_dihedral_angle_4_deg	18.218
r_dihedral_angle_3_deg	17.969
r_dihedral_angle_1_deg	6.577
r_scangle_it	2.132
r_angle_refined_deg	1.331
r_scbond_it	1.319
r_mcangle_it	0.778
r_mcbond_it	0.419
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.6
r_dihedral_angle_4_deg	18.218
r_dihedral_angle_3_deg	17.969
r_dihedral_angle_1_deg	6.577
r_scangle_it	2.132
r_angle_refined_deg	1.331
r_scbond_it	1.319
r_mcangle_it	0.778
r_mcbond_it	0.419
r_nbtor_refined	0.312
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.158
r_xyhbond_nbd_refined	0.143
r_metal_ion_refined	0.134
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12341
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

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.