3G02 | pdb_00003g02

Structure of enantioselective mutant of epoxide hydrolase from Aspergillus niger generated by directed evolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QO7	PDB ENTRY 1QO7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	20% PEG 6000, 0.1M MES, pH 6.0, 0.1M unbuffered sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.866	α = 90
b = 89.675	β = 104.79
c = 75.344	γ = 90

Symmetry
Space Group	P 1 21 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 4		2007-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.93300	ESRF	ID14-2

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	1.5	30.54	95.5	0.027	15.8	1.7	209428	120696

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)
	1.5	1.58	98.2		0.128	7.2	1.7	18142

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QO7	1.5	28.91	126958	120661	6102	95.04	0.184	0.184	0.183	0.18	0.204	0.2	RANDOM	15.23

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]
-0.36		-0.64	0.95		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.027
r_dihedral_angle_4_deg	13.791
r_dihedral_angle_3_deg	12.041
r_dihedral_angle_1_deg	5.416
r_scangle_it	1.75
r_scbond_it	1.143
r_angle_refined_deg	1.007
r_mcangle_it	0.759
r_mcbond_it	0.448
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.027
r_dihedral_angle_4_deg	13.791
r_dihedral_angle_3_deg	12.041
r_dihedral_angle_1_deg	5.416
r_scangle_it	1.75
r_scbond_it	1.143
r_angle_refined_deg	1.007
r_mcangle_it	0.759
r_mcbond_it	0.448
r_nbtor_refined	0.308
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.131
r_xyhbond_nbd_refined	0.102
r_symmetry_hbond_refined	0.08
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6354
Nucleic Acid Atoms
Solvent Atoms	715
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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.