7YU2

Structure of 6-aminohexanoate-oligomer hydrolase NylC, D122G/H130Y/T267C mutant, hydroxylamine-treated

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AXG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	283	1.4 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.27	α = 90
b = 144.022	β = 90
c = 128.262	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	CCD	RAYONIX MX225HE		2010-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9000	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.21	50	99.3	0.062	0.068	0.999	26.7	7		194470

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.21	1.23	93.2		0.65	0.745	0.791	2.04	4.1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3AXG	1.21	27.145	194260	9810	99.166	0.117	0.1157	0.1428	16.963

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]
1.547			-1.275		-0.272

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.205
r_dihedral_angle_4_deg	13.991
r_dihedral_angle_3_deg	11.745
r_rigid_bond_restr	7.498
r_dihedral_angle_1_deg	6.791
r_lrange_it	5.01
r_lrange_other	5.01
r_scangle_it	4.982
r_scangle_other	4.782
r_scbond_it	4.569
r_scbond_other	4.44
r_mcangle_it	2.81
r_mcangle_other	2.809
r_mcbond_it	2.387
r_mcbond_other	2.387
r_angle_refined_deg	2.105
r_angle_other_deg	1.641
r_nbd_other	0.288
r_symmetry_nbd_refined	0.271
r_nbd_refined	0.244
r_symmetry_nbd_other	0.212
r_symmetry_xyhbond_nbd_refined	0.197
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_other	0.173
r_chiral_restr	0.124
r_symmetry_nbtor_other	0.09
r_bond_refined_d	0.019
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4877
Nucleic Acid Atoms
Solvent Atoms	627
Heterogen Atoms	63

Software

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