2VZ4

The N-terminal domain of MerR-like protein TipAL bound to promoter DNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5		SITTING DROP CONTAINING 4 MICROLITERS PROTEIN-DNA SOLUTION PLUS 6 MICROLITERS RESERVOIR SOLUTION. PROTEIN-DNA SOLUTION: 500 MICROMOLAR (6 MILLIGRAMS/MILLILITER) PROTEIN, 275 MICROMOLAR DOUBLE-STRANDED DNA, 123 MILLIMOLAR SODIUM CHLORIDE, 16 MILLIMOLAR TRIS (TRIS(HYDROXYMETHYL)AMINOMETHANE), 8 MILLIMOLAR SODIUM CACODYLATE, 4 MILLIMOLAR MAGNESIUM CHLORIDE, 0.8 MILLIMOLAR EDTA (ETHYLENEDIAMINETETRAACETIC ACID), PH 8. RESERVOIR SOLUTION: 15% (WEIGHT/VOLUME) PEG-8K (POLY(ETHYLENE GLYCOL) WITH MOLECULAR MASS 8000 GRAMS/MOLE), 200 MILLIMOLAR MAGNESIUM CHLORIDE, 100 MILLIMOLAR TRIS (TRIS(HYDROXYMETHYL)AMINOMETHANE), PH 8.5.

Crystal Properties
Matthews coefficient	Solvent content
2.83	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.85	α = 90
b = 67.467	β = 90
c = 73.129	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	MARRESEARCH		2005-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	72.74	99.5	0.08	20.2	6.3		5321

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	3.06	99.5		0.35	5.5	6.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1R8D	2.9	30	4922	230	95.9	0.24	0.239	0.274	RANDOM	47.66

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]
1.5			-4.37		2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.988
r_dihedral_angle_4_deg	18.876
r_dihedral_angle_3_deg	15.313
r_dihedral_angle_1_deg	5.115
r_scangle_it	5.019
r_scbond_it	3.359
r_mcangle_it	2.385
r_mcbond_it	1.519
r_angle_refined_deg	1.337
r_angle_other_deg	0.912
r_symmetry_vdw_other	0.374
r_mcbond_other	0.342
r_nbd_refined	0.201
r_nbtor_refined	0.199
r_nbd_other	0.176
r_symmetry_vdw_refined	0.152
r_xyhbond_nbd_refined	0.122
r_nbtor_other	0.084
r_symmetry_hbond_refined	0.075
r_chiral_restr	0.051
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	794
Nucleic Acid Atoms	428
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing