3OR3 | pdb_00003or3

Restriction endonuclease HPY188I in complex with product DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OQG

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. CRYSTAL WAS SOAKED IN 0.1 M CaCl2 FOR 18 H., VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.395	α = 90
b = 65.395	β = 90
c = 221.783	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	2010-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.281	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	1.95	20	97.5	0.068	0.068	37.775	13.99	35348	35348			25.2

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)
	1.95	1.98	95.8		0.406	0.406	6.488	14.78	1348

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3OQG	1.95	20	35323	35323	1723	97.5	0.17013	0.17013	0.16849	0.17	0.20144	0.2	RESOLUTION SHELLS	22.527

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]
0.39			0.39		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.888
r_dihedral_angle_3_deg	14.622
r_dihedral_angle_4_deg	13.47
r_dihedral_angle_1_deg	5.795
r_angle_other_deg	3.943
r_scangle_it	2.161
r_scbond_it	1.551
r_angle_refined_deg	1.281
r_mcangle_it	1.182
r_mcbond_it	0.673
r_symmetry_vdw_other	0.249
r_symmetry_vdw_refined	0.246
r_nbd_other	0.232
r_symmetry_metal_ion_refined	0.231
r_symmetry_hbond_refined	0.198
r_nbd_refined	0.195
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.146
r_nbtor_other	0.112
r_chiral_restr	0.097
r_metal_ion_refined	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.012
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	2844
Nucleic Acid Atoms	365
Solvent Atoms	311
Heterogen Atoms	7

Software

Software
Software Name	Purpose
MAR345	data collection
ARP/wARP	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling