2BNW | pdb_00002bnw

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IRQ	PDB ENTRY 1IRQ AND 1CMA
experimental model	PDB	1CMA	PDB ENTRY 1IRQ AND 1CMA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		150 MM NA/KPO4, PH 7.0, 2.4 NA2MALONATE, PH 7.5, 2% AMINOCAPROIC ACID

Crystal Properties
Matthews coefficient	Solvent content
4	69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 219.426	α = 90
b = 44.631	β = 108.8
c = 75.96	γ = 90

Symmetry
Space Group	C 1 2 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		2004-10-28	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	2.45	30	97.4	0.06	12.7	3.3		83105		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	2.45	2.54	81.7		0.38	3	2.4

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 1IRQ AND 1CMA	2.45	43.44	24191	1044	97.2	0.227	0.226	0.23	0.26	0.27	RANDOM	45.81

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]
0.88		-1.1	1.44		-3.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.31
r_dihedral_angle_4_deg	21.229
r_dihedral_angle_3_deg	17.072
r_dihedral_angle_1_deg	5.761
r_scangle_it	1.426
r_angle_refined_deg	1.385
r_scbond_it	0.882
r_angle_other_deg	0.798
r_mcangle_it	0.663
r_mcbond_it	0.585
r_symmetry_hbond_refined	0.264
r_nbd_refined	0.214
r_nbtor_refined	0.211
r_nbd_other	0.203
r_xyhbond_nbd_refined	0.203
r_symmetry_vdw_other	0.188
r_symmetry_vdw_refined	0.181
r_nbtor_other	0.091
r_chiral_restr	0.053
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.003
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	1634
Nucleic Acid Atoms	1440
Solvent Atoms	79
Heterogen Atoms

Software

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