1EN7 | pdb_00001en7

ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		ENDOVII N62D MUTANT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2		HANGING DROP VAPOUR DIFFUSION 1 + 1 UL OF PROTEIN SOLUTION: 16 MG/ML ENDOVII, 175 MM NACL, 20 MM MGCL2, 2 MM ZNCL2, 10 MM 2-MERCAPTO-ETHANOL, 10 % GLYCEROL, 10 MM MOPS PH6.5; WELL: 16-18% PEG 5000 MME, 200 MM CACL2, 20 MM AMMONIUM SULPHATE, 10 MM 2-MERCAPTO-ETHANOL, 100 MM TRIS PH 8.2, ~ 1 MM SODIUM AZIDE, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.8	57.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.99	α = 90
b = 39.45	β = 106.2
c = 75.75	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	MARRESEARCH	NI COATED MIRRORS	1998-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS

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	2.33	44.281	99.4	0.06	11.8	3.8		17578			36.81

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)
	2.33	2.46	99.3		0.253	3	3.7

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-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	ENDOVII N62D MUTANT	2.4	10	15326	15326	828	99.5	0.2395	0.308	RANDOM	46.84

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	32.5
p_staggered_tor	15.2
p_planar_tor	5.5
p_scangle_it	3.301
p_mcangle_it	2.94
p_scbond_it	2.092
p_mcbond_it	1.955
p_multtor_nbd	0.268
p_singtor_nbd	0.177
p_xyhbond_nbd	0.177
p_chiral_restr	0.157
p_angle_d	0.032
p_bond_d	0.027
p_planar_d	0.024
p_angle_deg
p_hb_or_metal_coord
p_plane_restr
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2544
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	5

Software

Software
Software Name	Purpose
XDS	data scaling
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling