6F9O | pdb_00006f9o

Crystal structure of cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B6G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.88	293	0.2 M ammonium acetate, 30%(w/v) PEG 4000 and 0.1 M sodium acetate trihydrate pH 4.6 and with the addition of 0.6 ul of 0.1M L-proline (Additive Screen kit, Hampton Research) to the crystallization drop

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.332	α = 90
b = 79.451	β = 94.98
c = 43.489	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	RAYONIX MX-225	Sagitally bended Si111 crystal	2012-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.978260	BESSY	14.2

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	1.05	20	92.2	0.05	39.7	5.7		120315			16.716

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	1.05	1.09	56.2		0.307	3.4

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	1B6G	1.05	20	114202	6066	91.98	0.11139	0.11033	0.12	0.13151	0.14	RANDOM	8.671

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.671
r_sphericity_free	22.761
r_dihedral_angle_4_deg	16.682
r_dihedral_angle_3_deg	12.244
r_sphericity_bonded	7.178
r_dihedral_angle_1_deg	6.086
r_long_range_B_refined	2.693
r_long_range_B_other	2.693
r_rigid_bond_restr	2.273
r_angle_refined_deg	1.634
r_scangle_other	1.322
r_scbond_it	1.083
r_scbond_other	1.082
r_angle_other_deg	1.03
r_mcangle_it	1.023
r_mcangle_other	1.022
r_mcbond_it	0.71
r_mcbond_other	0.71
r_chiral_restr	0.097
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2465
Nucleic Acid Atoms
Solvent Atoms	576
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing