2EUV

Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MNN	PDB 1MNN - MINUS DNA AT SEQUENCE CHANGES AND 1 BASEPAIR ADJACENT TO THOSE CHANGES

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	30% PEG 400, 50 mM bis-tris-propane pH 7.0, 100 mM NaCl, 50 mM CaCl2, and 2 mM DTT. 1:1 Molar ratio protein:DNA, protein at 20mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.226	α = 90
b = 79.248	β = 90
c = 160.881	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	CCD	ADSC QUANTUM 210	MIRRORS	2003-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.072158	ALS	8.3.1

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	1.9	38.47	99.9	0.067	0.067	7.2	4.1	35256	35256

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)
	1.9	2	99.9		0.526	0.526	1.2	3.7	5080

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB 1MNN - MINUS DNA AT SEQUENCE CHANGES AND 1 BASEPAIR ADJACENT TO THOSE CHANGES	1.94	16.93	33048	33048	1645	99.81	0.195	0.195	0.193	0.233	RANDOM	26.702

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.619
r_scangle_it	2.652
r_scbond_it	1.69
r_angle_refined_deg	1.453
r_mcangle_it	1.437
r_angle_other_deg	0.884
r_mcbond_it	0.79
r_symmetry_hbond_refined	0.282
r_symmetry_vdw_other	0.244
r_xyhbond_nbd_refined	0.239
r_nbd_other	0.235
r_nbd_refined	0.175
r_symmetry_vdw_refined	0.167
r_nbtor_other	0.088
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2377
Nucleic Acid Atoms	513
Solvent Atoms	269
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling