3G38 | pdb_00003g38

The catalytically inactive mutant Mth0212 (D151N) in complex with an 8 bp dsDNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FZI	PDN ENTRY 3FZI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	reservoir: 5% (w/v) PEG 4000, 50mM KCl, 100mM MES pH 5.6, 10mM MgCl2; complex solution: 230mM NaCl, 8mM HEPES-KOH pH 7.6, 2mM MgCl2, 3mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.96	α = 90
b = 107.15	β = 90
c = 44.27	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	MAR CCD 165 mm		2007-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.80150	EMBL/DESY, HAMBURG	X11

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	2.74	36.424	100	0.117	0.117	5.881	7.6		10553			54.9

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	2.74	2.89	100		0.471	0.471	1.6	7.8	1497

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	PDN ENTRY 3FZI	3.04	34.13	7784	361	100	0.259	0.256	0.2536	0.328	0.3198	RANDOM	37.113

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]
-1.41			8.51		-7.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.893
r_dihedral_angle_3_deg	20.365
r_dihedral_angle_4_deg	19.194
r_dihedral_angle_1_deg	7.07
r_angle_refined_deg	1.381
r_nbtor_refined	0.316
r_symmetry_hbond_refined	0.266
r_nbd_refined	0.233
r_symmetry_vdw_refined	0.197
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2143
Nucleic Acid Atoms	326
Solvent Atoms	48
Heterogen Atoms	36

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection