2VKQ

Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CN1	PDB ENTRY 2CN1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				24% PEG1500, 20% GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.265	α = 90
b = 99.388	β = 90
c = 78.041	γ = 90

Symmetry
Space Group	C 2 2 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				2006-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.5	78.09	99.7	0.09	15	5.9		12172		-3

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	2.5	2.64	100		0.42	2.8	6.2

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	PDB ENTRY 2CN1	2.5	30	11573	570	99.5	0.211	0.21	0.242	RANDOM	46.09

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]
-1.22			1.61		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.976
r_dihedral_angle_4_deg	21.309
r_dihedral_angle_3_deg	13.99
r_dihedral_angle_1_deg	5.407
r_scangle_it	1.292
r_angle_refined_deg	1.039
r_scbond_it	0.869
r_angle_other_deg	0.82
r_mcangle_it	0.466
r_mcbond_it	0.399
r_xyhbond_nbd_refined	0.39
r_symmetry_vdw_other	0.246
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.183
r_nbtor_refined	0.173
r_nbd_other	0.167
r_symmetry_hbond_refined	0.096
r_nbtor_other	0.08
r_chiral_restr	0.057
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2188
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing