7YU1 | pdb_00007yu1

Structure of 6-aminohexanoate-oligomer hydrolase NylC precursor, D122G/H130Y/T267C 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
2.2	44.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.879	α = 90
b = 144.004	β = 90
c = 129.284	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 210		2010-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	1.13	50	99.5	0.055	0.059	0.999	33.9	7		240917

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	1.13	1.15	98.6		0.647	0.703	0.904	3.22	6.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3AXG	1.13	28.269	238908	12072	98.538	0.13	0.1288	0.14	0.1553	0.16	17.008

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]
2.529			-1.385		-1.144

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.472
r_dihedral_angle_4_deg	16.977
r_dihedral_angle_3_deg	11.194
r_dihedral_angle_1_deg	6.549
r_lrange_it	4.251
r_lrange_other	4.251
r_scangle_it	3.51
r_scangle_other	3.222
r_rigid_bond_restr	3.026
r_scbond_it	2.762
r_scbond_other	2.555
r_mcangle_it	1.962
r_mcangle_other	1.962
r_angle_refined_deg	1.807
r_mcbond_other	1.635
r_mcbond_it	1.634
r_angle_other_deg	1.591
r_nbd_other	0.326
r_symmetry_nbd_refined	0.322
r_metal_ion_refined	0.258
r_nbd_refined	0.221
r_symmetry_nbd_other	0.198
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.097
r_symmetry_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4877
Nucleic Acid Atoms
Solvent Atoms	732
Heterogen Atoms	54

Software

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