1RW9 | pdb_00001rw9

Crystal structure of the Arthrobacter aurescens chondroitin AC lyase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Hg-derivative of the same protein

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	293	PEG 8000, ammonium acetate, phosphate buffer, glycerol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.569	α = 90
b = 86.455	β = 106.9
c = 80.483	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 QUANTUM 4		2002-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.95	NSLS	X8C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	50	96.4	0.094	8.6	7.3	178066	178066	1	1

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	1.3	1.35	93.4		3.4

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	Hg-derivative of the same protein	1.35	36.04	158129	158129	1603	100	0.1307	0.13028	0.13	0.17503	0.17	RANDOM	13.903

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]
1.05		0.66	-0.26		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.765
r_dihedral_angle_4_deg	12.525
r_dihedral_angle_3_deg	10.636
r_sphericity_free	8.983
r_sphericity_bonded	7.594
r_dihedral_angle_1_deg	6.202
r_scangle_it	4.482
r_scbond_it	3.386
r_angle_other_deg	2.982
r_mcangle_it	2.792
r_mcbond_it	2.132
r_rigid_bond_restr	2.022
r_angle_refined_deg	1.973
r_symmetry_vdw_other	0.315
r_nbd_other	0.292
r_metal_ion_refined	0.28
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.197
r_symmetry_hbond_refined	0.187
r_symmetry_vdw_refined	0.167
r_chiral_restr	0.134
r_nbtor_other	0.104
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_gen_planes_other	0.008
r_bond_other_d	0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5596
Nucleic Acid Atoms
Solvent Atoms	1025
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling