Experiment: 6XY9

Crystal structure of haloalkane dehalogenase DbeA-M1 loop variant from Bradyrhizobium elkanii

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4K2A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	25% PEG 4000, 130 mM calcium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.89	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.75	α = 90
b = 75.13	β = 91.9
c = 77.6	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	MAR555 FLAT PANEL		2008-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.918	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.2	19.6	98.6	0.138	0.86	11.76	3.74		38810			32.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27			0.515	0.628	3.35

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	FREE R-VALUE	4k2a	2.2	19.6	36818	1938	98.91	0.1779	0.1749	0.1757	0.2354	0.2349	RANDOM	31.675

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]
-0.65		-1.04	1.93		-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.917
r_dihedral_angle_4_deg	19.41
r_dihedral_angle_3_deg	14.741
r_dihedral_angle_1_deg	6.423
r_angle_refined_deg	1.878
r_chiral_restr	0.128
r_bond_refined_d	0.019
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4647
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	12

Software

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