3G4T | pdb_00003g4t

Mth0212 (WT) in complex with a 7bp dsDNA

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	reservoir: 40mM MgAc/50mM sodium cacodylate pH 6.0/30% (v/v) MPD; complex solution: 50mM KCl, 10mM KH2PO4/K2HPO4 pH 7.0, 1mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.764	α = 90
b = 79.6	β = 90
c = 99.409	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		2008-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	1.00605	BESSY	14.2

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	2.64	50	97.9	0.047	36.2	7.6		23676

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	2.64	2.73	83.1		0.417	2.5	4.6

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 ENTRY 3FZI	2.64	42.57	22367	1213	97.42	0.24319	0.24046	0.24	0.29684	0.29	RANDOM	67.685

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]
2.78			-4.29		1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.088
r_dihedral_angle_3_deg	18.241
r_dihedral_angle_4_deg	17.209
r_dihedral_angle_1_deg	6.832
r_scangle_it	1.952
r_angle_refined_deg	1.335
r_mcangle_it	1.246
r_scbond_it	1.176
r_mcbond_it	0.708
r_nbtor_refined	0.314
r_symmetry_vdw_refined	0.298
r_symmetry_hbond_refined	0.227
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.09
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4248
Nucleic Acid Atoms	278
Solvent Atoms	16
Heterogen Atoms	17

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling