3G0R | pdb_00003g0r

Complex of Mth0212 and an 8bp dsDNA with distorted ends

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	5.6	293	reservoir: 189mM KCl, 9.5mM MgCl2, 4.7% (w/v) PEG 8000, 47mM MES/NaOH pH 5.6, 2.1% 1,4-butanediol, 2mM DTT; protein solution: 234mM NaCl, 7mM KHEPES pH 7.6, 1.83mM MgCl2, 2.7mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.751	α = 90
b = 80.76	β = 94.03
c = 105.211	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	CCD	MARMOSAIC 225 mm CCD		2007-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.97623	EMBL/DESY, HAMBURG	X12

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	2.4	50	92.8	0.061	22.7	4.7		27308

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	2.4	2.49	72.3		0.191	5.2	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-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	2.4	44.64	27293	1391	92.72	0.1811	0.17782	0.18	0.24286	0.24	RANDOM	27.829

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]
-0.7		1.12	-0.83		1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.675
r_dihedral_angle_4_deg	18.71
r_dihedral_angle_3_deg	18.102
r_dihedral_angle_1_deg	7.201
r_scangle_it	2.84
r_scbond_it	1.788
r_angle_refined_deg	1.586
r_mcangle_it	1.328
r_mcbond_it	0.698
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.209
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.099
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
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_refined
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	4252
Nucleic Acid Atoms	423
Solvent Atoms	305
Heterogen Atoms	113

Software

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