2RBF | pdb_00002rbf

Structure of the ribbon-helix-helix domain of Escherichia coli PutA (PutA52) complexed with operator DNA (O2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AY0	PDB entry 2AY0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	30% PEG-MME 550, 50 mM CaCl2, and 100 mM Bis-Tris pH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.911	α = 90
b = 44.084	β = 101.5
c = 55.23	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	NOIR-1		2006-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.24	ALS	4.2.2

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	2.25	54.153	99.5	0.059	0.059	8.2	3.6		10293

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	2.25	2.37	99.3		0.434	0.434	1.6	3.6	1488

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2AY0	2.25	54.15	10293	10293	524	99.29	0.208	0.208	0.206	0.21	0.246	0.24	RANDOM	44.736

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]
-1.48		0.22	0.82		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.617
r_dihedral_angle_4_deg	19.637
r_dihedral_angle_3_deg	15.653
r_dihedral_angle_1_deg	5.638
r_scangle_it	2.056
r_angle_refined_deg	1.591
r_scbond_it	1.404
r_mcangle_it	1.157
r_angle_other_deg	1.089
r_mcbond_it	0.631
r_symmetry_vdw_other	0.237
r_nbtor_refined	0.208
r_nbd_other	0.188
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.181
r_nbd_refined	0.175
r_mcbond_other	0.148
r_nbtor_other	0.078
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_symmetry_hbond_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	709
Nucleic Acid Atoms	757
Solvent Atoms	27
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
CNS	phasing