1ZTV

Crystal structure of a duf72 family protein (ef0366) from enterococcus faecalis v583 at 3.10 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VPY	pdb entry 1vpy

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	6.5	277	1.0M NaCitrate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.08	69.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.819	α = 90
b = 92.358	β = 90
c = 119.347	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315	Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing)	2004-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	3.1	119.52	99.4	0.08	0.08	8.6	3.4		18876

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	3.1	3.27		99.7	0.392	0.392	1.9	3.5

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-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR	THROUGHOUT	pdb entry 1vpy	3.1	73.13	17862	975	100	0.193	0.19257	0.191	0.224	RANDOM	77.153

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]
-0.99			-1.31		2.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.674
r_dihedral_angle_3_deg	11.289
r_dihedral_angle_4_deg	9.97
r_dihedral_angle_1_deg	4.42
r_scangle_it	3.46
r_scbond_it	2.268
r_mcangle_it	1.376
r_mcbond_it	0.809
r_angle_refined_deg	0.647
r_angle_other_deg	0.539
r_symmetry_hbond_refined	0.248
r_nbd_refined	0.201
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.186
r_nbd_other	0.171
r_mcbond_other	0.147
r_symmetry_vdw_other	0.125
r_symmetry_vdw_refined	0.12
r_nbtor_other	0.084
r_xyhbond_nbd_other	0.06
r_chiral_restr	0.059
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4419
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing