2EVH | pdb_00002evh

Structure of a Ndt80-DNA complex (MSE mutant mA7G)

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 5 mM DTT. 1:1 Molar ratio protein:DNA, protein at 15 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.534	α = 90
b = 78.441	β = 90
c = 161.334	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	95	CCD	SBC-2		2001-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.0093	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.989	43.8	97.23			29735	29735

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.989	2.12	93.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	1.989	43.8	29873	29873	1508	97.23	0.18	0.18	0.179	0.21	0.212	0.23	RANDOM	19.278

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]
-0.01					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.656
r_scangle_it	2.192
r_scbond_it	1.402
r_angle_refined_deg	1.331
r_mcangle_it	1.242
r_angle_other_deg	1.121
r_mcbond_it	0.678
r_symmetry_hbond_refined	0.369
r_symmetry_vdw_other	0.275
r_symmetry_vdw_refined	0.244
r_nbd_other	0.236
r_xyhbond_nbd_refined	0.209
r_nbd_refined	0.179
r_nbtor_other	0.086
r_chiral_restr	0.075
r_bond_refined_d	0.008
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	2401
Nucleic Acid Atoms	551
Solvent Atoms	300
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