3BOS

Crystal structure of a putative dna replication regulator HDA (SAMA_1916) from Shewanella amazonensis sb2b at 1.75 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	277	NANODROP, 0.2M Sodium thiocyanate, 20% PEG 3350, No Buffer pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.037	α = 90
b = 64.032	β = 90
c = 153.64	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-11-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97932, 0.91837	SSRL	BL11-1

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	1.75	29.553	99.7	0.102	0.102	5.2	3.7		55436			19.79

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	1.75	1.8	100		0.643	0.643	1.2	3.7	4067

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.75	29.553	55402	2813	99.54	0.168	0.166	0.201	RANDOM	16.815

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]
-0.12			0.74		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.638
r_dihedral_angle_4_deg	15.132
r_dihedral_angle_3_deg	12.442
r_scangle_it	6.212
r_dihedral_angle_1_deg	4.491
r_scbond_it	4.456
r_mcangle_it	2.551
r_mcbond_it	1.585
r_angle_refined_deg	1.474
r_angle_other_deg	0.98
r_mcbond_other	0.72
r_symmetry_vdw_refined	0.494
r_symmetry_vdw_other	0.351
r_nbd_refined	0.231
r_nbd_other	0.201
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.175
r_symmetry_hbond_refined	0.146
r_metal_ion_refined	0.117
r_chiral_restr	0.087
r_nbtor_other	0.086
r_bond_refined_d	0.014
r_xyhbond_nbd_other	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3574
Nucleic Acid Atoms
Solvent Atoms	554
Heterogen Atoms	113

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing