3GOX | pdb_00003gox

Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I in the absence of EDTA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.1 M HEPES/Sodium hydroxide pH 7.5, 0.1 M Sodium chloride, 30 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.682	α = 90
b = 90.682	β = 90
c = 334.933	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	100	CCD	MARRESEARCH		2008-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	1.5	20	99.6	0.04	16.62	3.6	84393	84393			16.2

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	1.5	1.54	99.9		0.335	3.9	3.57

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.5	19.6	84392	84392	4298	99.64	0.16964	0.16873	0.19	0.18639	0.21	RANDOM	17.11

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]
-0.12	-0.06		-0.12		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.849
r_dihedral_angle_4_deg	15.246
r_dihedral_angle_3_deg	12.661
r_dihedral_angle_1_deg	5.965
r_angle_other_deg	3.95
r_scangle_it	2.663
r_scbond_it	1.693
r_angle_refined_deg	1.207
r_mcangle_it	1.171
r_mcbond_it	0.626
r_symmetry_vdw_refined	0.336
r_symmetry_vdw_other	0.269
r_nbd_other	0.236
r_nbd_refined	0.203
r_nbtor_refined	0.186
r_symmetry_metal_ion_refined	0.149
r_metal_ion_refined	0.147
r_xyhbond_nbd_refined	0.117
r_symmetry_hbond_refined	0.117
r_nbtor_other	0.107
r_chiral_restr	0.08
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_gen_planes_other	0.007
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
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	2982
Nucleic Acid Atoms	405
Solvent Atoms	476
Heterogen Atoms	23

Software

Software
Software Name	Purpose
MxCuBE	data collection
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling