3CNG | pdb_00003cng

Crystal structure of NUDIX hydrolase from Nitrosomonas europaea

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	294	0.1 M Bis-Tris, 0.2 M Magnesium chloride, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.781	α = 90
b = 49.506	β = 106.28
c = 110.19	γ = 90

Symmetry
Space Group	C 1 2 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 QUANTUM 315		2007-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97920	APS	19-ID

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	37.2	83	0.087	11.5	6.7	51323	51323			40.8

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	2.05	47.8		0.506	2.05	4.6	2106

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	SAD	THROUGHOUT	2	37.2	51312	51312	2582	82.94	0.183	0.183	0.181	0.1845	0.233	0.2353	RANDOM	35.641

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]
-1.92		-0.11	3.51		-1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.08
r_dihedral_angle_4_deg	17.869
r_dihedral_angle_3_deg	16.585
r_dihedral_angle_1_deg	6.739
r_scangle_it	3.921
r_scbond_it	2.536
r_angle_refined_deg	1.668
r_mcangle_it	1.554
r_angle_other_deg	0.989
r_mcbond_it	0.865
r_symmetry_vdw_other	0.286
r_mcbond_other	0.22
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.208
r_nbd_other	0.204
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.177
r_symmetry_hbond_refined	0.128
r_metal_ion_refined	0.113
r_chiral_restr	0.106
r_nbtor_other	0.09
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5774
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	49

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing