1NWW | pdb_00001nww

Limonene-1,2-epoxide hydrolase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Model from structure solution using SAD on Se-Met labelled protein. SAD data collected at ESRF beamline ID14-1 at 0.934 A wavelength.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	PEG 6000, LiCl, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.548	α = 90
b = 47.652	β = 90
c = 129.701	γ = 90

Symmetry
Space Group	P 21 21 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 4		1999-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.931	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	64.6	99.7	0.063	28.2	4.1	89183	88916

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.2	1.21	94.1		0.272	3.5	2.3

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	SAD	THROUGHOUT	Model from structure solution using SAD on Se-Met labelled protein. SAD data collected at ESRF beamline ID14-1 at 0.934 A wavelength.	1.2	50	84491	84491	4306	100	0.14822	0.14822	0.14686	0.15	0.17451	0.17	RANDOM	13.873

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]
0.32			-0.01		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.784
r_sphericity_free	15.439
r_sphericity_bonded	6.679
r_dihedral_angle_1_deg	6.02
r_scangle_it	5.31
r_scbond_it	3.739
r_angle_other_deg	3.181
r_mcangle_it	2.778
r_angle_refined_deg	2.384
r_mcbond_it	1.899
r_rigid_bond_restr	1.825
r_symmetry_vdw_refined	0.569
r_nbtor_other	0.274
r_symmetry_vdw_other	0.272
r_symmetry_hbond_refined	0.224
r_nbd_refined	0.217
r_nbd_other	0.199
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.127
r_xyhbond_nbd_other	0.064
r_bond_refined_d	0.023
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2305
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
MLPHARE	phasing