3OQG | pdb_00003oqg

Restriction endonuclease HPY188I in complex with substrate DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	292	0.1 M MES/NaOH pH 6.2 and 30% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.236	α = 90
b = 65.236	β = 90
c = 220.63	γ = 90

Symmetry
Space Group	P 41 21 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	BENT MIRROR	2010-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

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	1.75	20	98	0.061	0.061	24.651	5.55	48330	48330			23.2

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)
	1.75	1.77	97.1		0.44	0.44	3.265	5.55	1895

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 (All)	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	MAD	THROUGHOUT	1.75	19.9	48287	48287	2393	98	0.16612	0.16612	0.16474	0.1682	0.19218	0.1936	RESOLUTION SHELLS	20.972

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]
0.7			0.7		-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.222
r_dihedral_angle_3_deg	15.094
r_dihedral_angle_4_deg	13.779
r_dihedral_angle_1_deg	5.58
r_angle_other_deg	3.961
r_scangle_it	2.251
r_scbond_it	1.492
r_angle_refined_deg	1.224
r_mcangle_it	1.107
r_mcbond_it	0.6
r_nbd_other	0.23
r_symmetry_vdw_other	0.23
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.208
r_nbtor_refined	0.191
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_other	0.156
r_xyhbond_nbd_refined	0.151
r_nbtor_other	0.112
r_chiral_restr	0.077
r_metal_ion_refined	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.008
r_bond_other_d
r_metal_ion_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	2894
Nucleic Acid Atoms	363
Solvent Atoms	359
Heterogen Atoms	3

Software

Software
Software Name	Purpose
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing