2BNZ

Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to inverted DNA heptad repeats

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		120 MM NA/KPO4, PH 7.2, 2.2 M DINATRIUMMALONATE, PH 7.5, 3 % 2-METHYL-2,4-PENTANDIOL

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.991	α = 90
b = 42.505	β = 107.17
c = 103.727	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	MARRESEARCH		2004-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

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	2.6	35	92.8	0.11	11.7	2.5		18516		1

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	2.6	2.69	72.2		0.29	3.1	1.9

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 2BNW	2.6	100	17564	944	92.8	0.227	0.225	0.258	RANDOM	34.17

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]
-1.18		2.27	0.1		2.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.312
r_dihedral_angle_4_deg	18.49
r_dihedral_angle_3_deg	17.026
r_dihedral_angle_1_deg	6.435
r_mcangle_it	1.051
r_angle_refined_deg	1.044
r_scangle_it	1.035
r_mcbond_it	0.878
r_angle_other_deg	0.727
r_scbond_it	0.554
r_symmetry_hbond_refined	0.217
r_xyhbond_nbd_refined	0.209
r_nbd_refined	0.208
r_nbtor_refined	0.206
r_nbd_other	0.2
r_symmetry_vdw_other	0.181
r_symmetry_vdw_refined	0.11
r_nbtor_other	0.088
r_chiral_restr	0.051
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
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_mcbond_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	1613
Nucleic Acid Atoms	927
Solvent Atoms	45
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing