1OFL

CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE HEXASACCHARIDE

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.7		PEG8000, 2-METHYL-2,4- PENTADIOL, AMMONIUM ACETATE, TRIS, pH 8.70

Crystal Properties
Matthews coefficient	Solvent content
1.95	34.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.574	α = 90
b = 73.989	β = 93.93
c = 59.063	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC CCD		2000-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C		NSLS	X8C

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	1.7	34.98	92.5	0.041	16.5	2.85		44254

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	1.7	1.76	65.3		0.149	5.5

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	PDB ENTRY 1DBG	1.7	40	42015	2211	92.5	0.135	0.133	0.14	0.176	0.18	RANDOM	13.47

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]
0.02		-0.25	-0.02		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.783
r_dihedral_angle_4_deg	16.062
r_dihedral_angle_3_deg	12.615
r_dihedral_angle_1_deg	6.922
r_scangle_it	4.312
r_scbond_it	2.789
r_angle_refined_deg	1.839
r_mcangle_it	1.725
r_mcbond_it	1.013
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.214
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.14
r_metal_ion_refined	0.081
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3784
Nucleic Acid Atoms
Solvent Atoms	757
Heterogen Atoms	196

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing