3V8E | pdb_00003v8e

Crystal structure of the yeast nicotinamidase Pnc1p bound to the inhibitor nicotinaldehyde

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	Protein was dialyzed against buffer containing 15 mM Tris pH 7.5, 50 mM NaCl, 4 mM MgCl2, 10 mM Na Citrate and 5 % glycerol and the inhibitor nicotinaldehyde was added at a 4:1 ratio. The protein (5 mg/ml) was mixed with mother liquor (1.6 M NaOAc, 10 % ethylene glycol, 0.1 M HEPES pH 7.4) at a 1:1 (vol) ratio. Crystals were formed by hanging drop vapor diffusion. Crystals were transferred to a cryoprotectant solution (1.5 M NaOAc, 20% ethylene glycol, 0.1M HEPES pH 7.4) and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 298.717	α = 90
b = 298.717	β = 90
c = 112.652	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	MARMOSAIC 225 mm CCD		2009-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	30	100		5.7	101157	101147

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	2.7	2.75	100		0.348	5.3	5.5

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		THROUGHOUT	2.71	30	96087	5058	99.71	0.18221	0.18108	0.1805	0.2031	0.2023	RANDOM	57.356

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]
0.68	0.34		0.68		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.035
r_dihedral_angle_3_deg	17.253
r_dihedral_angle_4_deg	15.903
r_dihedral_angle_1_deg	6.207
r_angle_refined_deg	1.204
r_chiral_restr	0.088
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12397
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement