7YU0

Structure of 6-aminohexanoate-oligomer hydrolase NylC precursor, H130Y/N266A/T267A mutant

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
2.22	44.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.242	α = 90
b = 144.345	β = 90
c = 129.178	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	ADSC QUANTUM 270		2009-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0000	Photon Factory	BL-17A

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	1.35	50	98	0.074	0.077	0.999	30.4	12.5		140625

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	1.35	1.37	82		0.499	0.526	0.94	3.35	8.7

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	1.35	37.006	140512	7049	97.716	0.112	0.1106	0.1394	21.236

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]
1.836			-1.831		-0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.019
r_dihedral_angle_4_deg	14.717
r_dihedral_angle_3_deg	11.66
r_dihedral_angle_1_deg	6.796
r_lrange_it	3.493
r_lrange_other	3.493
r_scangle_it	3.019
r_scangle_other	2.782
r_scbond_it	2.654
r_scbond_other	2.396
r_mcangle_it	1.913
r_mcangle_other	1.913
r_rigid_bond_restr	1.706
r_mcbond_it	1.581
r_mcbond_other	1.581
r_angle_other_deg	1.498
r_angle_refined_deg	1.492
r_symmetry_nbd_refined	0.23
r_nbd_other	0.226
r_nbd_refined	0.209
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.167
r_metal_ion_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.145
r_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4864
Nucleic Acid Atoms
Solvent Atoms	579
Heterogen Atoms	88

Software

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