4IHT | pdb_00004iht

Crystal Structure of BenM_DBD/benA site 1 DNA Complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M1E	PDB entry 3M1E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER OIL	6.5	288	Equal volumes of precipitant, protein solution and DNA. Precipitant: Optimized index screen 79- 25 mM bis-tris, 25% PEG 3000, 50 mM ammonium acetate. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% glycerol, 150 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.956	α = 90
b = 300.295	β = 90
c = 46.003	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		2009-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	APS	19-ID

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	2.9	50	92.7	0.065	21.1	3.7		17712			99.4

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	2.9	2.95	92.9		0.503		3.3	875

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 3M1E	3	31.66	15998	820	92.52	0.1877	0.1845	0.1845	0.2452	0.2484	RANDOM	95.0928

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]
8.54			-2.54		-6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.475
r_dihedral_angle_3_deg	17.601
r_dihedral_angle_4_deg	16.114
r_dihedral_angle_1_deg	5.289
r_angle_refined_deg	1.143
r_angle_other_deg	0.842
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2872
Nucleic Acid Atoms	2038
Solvent Atoms	3
Heterogen Atoms

Software

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