4YUB

Crystal structure of human Nicotinic Acid Phosphoribosyltransferase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.1 M Sodium cacodylate pH 6.5 and 1.7 M Sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.018	α = 90
b = 101.091	β = 90
c = 125.144	γ = 90

Symmetry
Space Group	P 21 21 21

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		2013-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.972	ESRF	ID23-2

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	2.9	58.64	99.7	0.011	10	4.4		25261

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	2.9		99.3		0.037	3.7	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	2F7F	2.9	50	25137	124	99.48	0.19711	0.19689	0.24285	RANDOM	41.616

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]
-1.23			4.24		-3.01

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	11.955
r_long_range_B_other	11.951
r_mcangle_it	6.346
r_mcangle_other	6.346
r_scangle_other	6.245
r_mcbond_it	3.691
r_mcbond_other	3.691
r_scbond_it	3.563
r_scbond_other	3.562
r_angle_refined_deg	1.832
r_angle_other_deg	1.021
r_chiral_restr	0.156
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7558
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MR-Rosetta	phasing
SCALA	data scaling
XDS	data reduction
XDS	data scaling