4WDR | pdb_00004wdr

Crystal structure of haloalkane dehalogenase LinB 140A+143L+177W+211L mutant (LinB86) from Sphingobium japonicum UT26

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WDQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1M MOPS, 0.1M HEPES; 0.3M MgCl2; 0.3M CaCl2; 20% PEG550MME; 10%PEG20K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.937	α = 90
b = 125.937	β = 90
c = 213.818	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2013-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.972386	ESRF	ID29

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	2.5	50	99.7	14.66	7.81	22938	22874

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	2.5	2.65	98.7		0.87	2.14

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	4WDQ	2.5	48.58	1144	99.72	0.1667	0.1651	0.17	0.1959	0.2	RANDOM	59.36

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]
0.18	0.09		0.18		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.77
r_dihedral_angle_4_deg	19.475
r_dihedral_angle_3_deg	15.837
r_dihedral_angle_1_deg	5.827
r_mcangle_it	3.023
r_mcbond_it	2.018
r_mcbond_other	2.018
r_angle_refined_deg	1.602
r_angle_other_deg	1.058
r_chiral_restr	0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.77
r_dihedral_angle_4_deg	19.475
r_dihedral_angle_3_deg	15.837
r_dihedral_angle_1_deg	5.827
r_mcangle_it	3.023
r_mcbond_it	2.018
r_mcbond_other	2.018
r_angle_refined_deg	1.602
r_angle_other_deg	1.058
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4609
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction
Coot	model building
SCALEPACK	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.