4WDQ | pdb_00004wdq

Crystal structure of haloalkane dehalogenase LinB32 mutant (L177W) from Sphingobium japonicum UT26

X-RAY DIFFRACTION

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	5.6	295	0.1M MES; 0.2M MgCl2; 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.729	α = 90
b = 68.49	β = 90
c = 81.055	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	MAR CCD 165 mm		2011-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8123	EMBL/DESY, HAMBURG	X13

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	1.57	50	98.3	0.094	6.5	6.9	37131	36500

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	1.57	1.63	85.2		0.285		5.4	3111

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	1.58	40.49	36137	1802	98.55	0.1619	0.1596	0.16	0.2057	0.21	RANDOM	12.777

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]
0.01					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.3
r_dihedral_angle_4_deg	18.692
r_dihedral_angle_3_deg	11.899
r_dihedral_angle_1_deg	5.993
r_scangle_it	2.686
r_scbond_it	1.762
r_angle_refined_deg	1.399
r_mcangle_it	1.005
r_mcbond_it	0.716
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.3
r_dihedral_angle_4_deg	18.692
r_dihedral_angle_3_deg	11.899
r_dihedral_angle_1_deg	5.993
r_scangle_it	2.686
r_scbond_it	1.762
r_angle_refined_deg	1.399
r_mcangle_it	1.005
r_mcbond_it	0.716
r_nbtor_refined	0.314
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.184
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.097
r_metal_ion_refined	0.016
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2353
Nucleic Acid Atoms
Solvent Atoms	714
Heterogen Atoms	5

Software

Software
Software Name	Purpose
HKL-3000	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
HKL-3000	data scaling

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.