2YX2 | pdb_00002yx2

Crystal structure of cloned trimeric hyluranidase from streptococcus pyogenes at 2.8 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C3F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	TRIS HCL, SODIUM FORMATE, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.77	α = 90
b = 58.77	β = 90
c = 586.241	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	MARRESEARCH	Mirror	2006-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	0.803	EMBL/DESY, HAMBURG	X31

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	2.8	20	99.8	0.058	6.7		10238	10238

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.84	99.8		0.308	2.1

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2C3F	2.8	20	10238	9744	494	99.57	0.19554	0.19471	0.19227	0.22397	RANDOM	51.155

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]
2.79	1.4		2.79		-4.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.761
r_dihedral_angle_4_deg	22.381
r_dihedral_angle_3_deg	18.271
r_dihedral_angle_1_deg	6.781
r_scangle_it	5.522
r_scbond_it	3.556
r_mcangle_it	2.645
r_angle_refined_deg	1.645
r_mcbond_it	1.583
r_nbtor_refined	0.321
r_symmetry_vdw_refined	0.256
r_nbd_refined	0.249
r_symmetry_hbond_refined	0.2
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
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_refined
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	2515
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing