4H77 | pdb_00004h77

Crystal structure of haloalkane dehalogenase LinB from Sphingobium sp. MI1205

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CV2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	278	100mM Tris-HCl (pH 8.0), 20% (w/v) PEG 4000, 200mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.404	α = 90
b = 72.146	β = 90
c = 73.492	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray					2008-06-07

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)	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	1.6	20					36060

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 (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	1CV2	1.6	20	34221	1797	99.9	0.16026	0.15863	0.17	0.19101	0.19	RANDOM	8.176

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]
-0.52			0.07		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.247
r_dihedral_angle_4_deg	14.098
r_dihedral_angle_3_deg	13.328
r_dihedral_angle_1_deg	5.445
r_scangle_it	2.785
r_scbond_it	1.716
r_angle_refined_deg	1.371
r_mcangle_it	0.974
r_mcbond_it	0.81
r_nbtor_refined	0.317
r_symmetry_vdw_refined	0.213
r_symmetry_hbond_refined	0.211
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.092
r_metal_ion_refined	0.076
r_symmetry_metal_ion_refined	0.012
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2332
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	21

Software

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