3VWN | pdb_00003vwn

Crystal structure of 6-aminohexanoate-dimer hydrolase G181D/R187G/H266N/D370Y mutant

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	283	2.2M AMMONIUM SULFATE, 0.2M LITHIUM SULFATE, 0.1M MES, pH 6.5, vapor diffusion, sitting drop, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.64	α = 90
b = 96.64	β = 90
c = 112.996	γ = 120

Symmetry
Space Group	P 32 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 270		2009-10-23	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)	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	1.2	50	100	0.058	18.3	10.1		189410		-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	1.2	1.22	99.8		0.536		5.7	9366

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	FOURIER SYNTHESIS	THROUGHOUT	1.2	50	189172	9503	99.79	0.1303	0.1295	0.14	0.1458	0.15	RANDOM	21.6356

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]
0.07	0.04		0.07		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.901
r_dihedral_angle_4_deg	19.257
r_dihedral_angle_3_deg	11.297
r_scangle_it	8.619
r_dihedral_angle_1_deg	6.061
r_scbond_it	6.034
r_mcangle_it	4.632
r_rigid_bond_restr	3.432
r_mcbond_it	3.361
r_angle_refined_deg	2.361

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.901
r_dihedral_angle_4_deg	19.257
r_dihedral_angle_3_deg	11.297
r_scangle_it	8.619
r_dihedral_angle_1_deg	6.061
r_scbond_it	6.034
r_mcangle_it	4.632
r_rigid_bond_restr	3.432
r_mcbond_it	3.361
r_angle_refined_deg	2.361
r_chiral_restr	0.391
r_bond_refined_d	0.028
r_gen_planes_refined	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2958
Nucleic Acid Atoms
Solvent Atoms	429
Heterogen Atoms	84

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.