2AY0 | pdb_00002ay0

Structure of the Lys9Met mutant of the E. coli Proline Utilization A (PutA) DNA-binding domain.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	1.7-3.0 M NaCl, 5 mM dithiothreitol, pH 3.0-5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.07	α = 90
b = 91.494	β = 119.21
c = 69.606	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	173	CCD	CUSTOM-MADE		2004-12-08	M	MAD
2	1
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	0.987121, 0.979553, 0.979144	ALS	4.2.2

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	60.75	100	0.079	12.5	7.47	26606	26606

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	2.07			0.52	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MAD	THROUGHOUT	2.1	60.75	26606	21873	1153	99.88	0.20597	0.204	0.21	0.2418	0.25	RANDOM	38.245

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]
0.61		-0.67	0.11		-1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.346
r_dihedral_angle_3_deg	15.652
r_dihedral_angle_4_deg	14.232
r_dihedral_angle_1_deg	4.667
r_scangle_it	2.473
r_scbond_it	1.637
r_angle_refined_deg	1.139
r_mcangle_it	1.007
r_angle_other_deg	0.774
r_mcbond_it	0.732
r_symmetry_vdw_refined	0.253
r_nbd_refined	0.219
r_nbtor_refined	0.171
r_nbd_other	0.167
r_symmetry_vdw_other	0.167
r_xyhbond_nbd_refined	0.147
r_mcbond_other	0.137
r_symmetry_hbond_refined	0.097
r_nbtor_other	0.082
r_chiral_restr	0.069
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2072
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	6

Software

Software
Software Name	Purpose
d*TREK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection