2Q1F | pdb_00002q1f

Crystal structure of chondroitin sulfate lyase abc from bacteroides thetaiotaomicron wal2926

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	282	17% PEG 3350, 0.2M ammonium sulfate, 100 mM HEPES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 223.362	α = 90
b = 223.362	β = 90
c = 112.639	γ = 120

Symmetry
Space Group	P 63

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	MARMOSAIC 300 mm CCD	DOUBLE-CRYSTAL FIXED-EXIT SI- 111 MONOCHROMATOR (E/E~10-4) AND A PLANAR PALLADIUM-COATED SILICON MIRROR	2006-05-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.85	50	94.7	0.063	0.05	14.6	3.1		71079

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.85	2.92	56.7		0.4	0.326	1.6	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.85	50	67482	3599	94.8	0.222	0.22	0.2115	0.262	0.2516	RANDOM	59.33

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]
-1.88	-0.94		-1.88		2.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.854
r_dihedral_angle_3_deg	17.472
r_dihedral_angle_4_deg	15.287
r_dihedral_angle_1_deg	5.167
r_scangle_it	1.864
r_mcangle_it	1.214
r_scbond_it	1.195
r_angle_refined_deg	1.007
r_mcbond_it	0.826
r_nbtor_refined	0.3
r_nbd_refined	0.189
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.111
r_metal_ion_refined	0.073
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15824
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	82

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHARP	phasing