4LXG | pdb_00004lxg

Crystal structure of DxnB2, a carbon - carbon bond hydrolase from Sphingomonas wittichii RW1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J1I	PDB ENTRY 1J1I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.2	293	grid of ammonium sulfate (1.0-2.5 M) containing 0.1 M Tris, pH 8.2 and 6-10% ethanol, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.983	α = 90
b = 66.983	β = 90
c = 327.743	γ = 120

Symmetry
Space Group	P 65 2 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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	1	APS	14-BM-C

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	2.2	58.03	99.5			22668	22668	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.2	99.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1J1I	2.22	36.46	22668	22550	1150	99.48	0.2033	0.2017	0.1991	0.2336	0.2319	RANDOM	52.9638

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]
0.75	0.75		0.75		-2.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.9
r_dihedral_angle_3_deg	13.502
r_dihedral_angle_4_deg	12.295
r_dihedral_angle_1_deg	5.141
r_scbond_it	3.465
r_mcangle_it	3.144
r_mcbond_it	2.129
r_angle_refined_deg	1.017
r_chiral_restr	0.064
r_bond_refined_d	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2090
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	15

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling