1E7D | pdb_00001e7d

Endonuclease VII (ENDOVII) Ffrom Phage T4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E7L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2		HANGING DROP VAPOUR DIFFUSION DROP SIZE: 1 + 1 UL 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, C.A. 1 MM SODIUM AZIDE

Crystal Properties
Matthews coefficient	Solvent content
2.18	44.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.9	α = 90
b = 37.4	β = 108.2
c = 74	γ = 90

Symmetry
Space Group	P 1 21 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	1999-01-15	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	2.8	44.281	99.8	0.096	7.2	3.2		8966

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	2.9	99.7		0.283	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	1E7L	2.8	10	8966	413	99.8	0.245	0.23	0.315	0.3	RANDOM

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	30.4
p_staggered_tor	18.2
p_planar_tor	5.9
p_scangle_it	3.6
p_mcangle_it	3.3
p_scbond_it	2.3
p_mcbond_it	2.1
p_multtor_nbd	0.263
p_singtor_nbd	0.185
p_planar_d	0.031
p_angle_d	0.022
p_bond_d	0.015
p_plane_restr	0.009
p_angle_deg
p_hb_or_metal_coord
p_chiral_restr
p_xhyhbond_nbd
p_xyhbond_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	30
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
AMoRE	phasing