3IRH | pdb_00003irh

Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dATP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O6I	PDB ID 2O6I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	295	0.2 M Sodium bromide, 0.1 M Bis-tris propane pH 7.5, 20 % w/v Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.253	α = 90
b = 188.66	β = 90
c = 67.822	γ = 90

Symmetry
Space Group	P 21 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	BERYLLIUM LENSES/DIAMOND LAUE MONO	2008-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F		APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.4	30	99.1	0.08	21	3.9		75951		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	95.3		0.55	2.4	1.9

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 (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	PDB ID 2O6I	2.4	30	71324	3783	99.2	0.188	0.185	0.19	0.244	0.18	RANDOM	40.67

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]
-5.12			2.09		3.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.703
r_dihedral_angle_4_deg	16.627
r_dihedral_angle_3_deg	15.873
r_dihedral_angle_1_deg	5.493
r_scangle_it	3.06
r_scbond_it	1.907
r_mcangle_it	1.211
r_angle_refined_deg	1.21
r_mcbond_it	0.693
r_nbtor_refined	0.304
r_metal_ion_refined	0.245
r_nbd_refined	0.204
r_symmetry_hbond_refined	0.201
r_symmetry_vdw_refined	0.197
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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	14635
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms	188

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling