2RKH

Crystal structure of a putative AphA-like transcription factor (ZP_00208345.1) from Magnetospirillum magnetotacticum MS-1 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	NANODROP, 15.0% Glycerol, 0.17M NaOAc, 25.5% PEG 4000, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.62	α = 90
b = 66.62	β = 90
c = 92.6	γ = 90

Symmetry
Space Group	P 43 21 2

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	ADSC QUANTUM 315		2007-09-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0000, 0.9795, 0.9797	ALS	8.2.1

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	28.364	99.7	0.046	16.26			14688		-3	44.566

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	97.4		0.665	2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	28.364	14640	736	99.79	0.214	0.212	0.21	0.256	0.25	RANDOM	39.306

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]
-0.27			-0.27		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.38
r_dihedral_angle_4_deg	13.118
r_dihedral_angle_3_deg	10.605
r_scangle_it	5.758
r_scbond_it	4.326
r_dihedral_angle_1_deg	3.608
r_mcangle_it	2.621
r_mcbond_it	2.035
r_angle_refined_deg	1.456
r_angle_other_deg	1.341
r_mcbond_other	0.392
r_nbd_refined	0.187
r_symmetry_vdw_other	0.175
r_nbtor_refined	0.139
r_symmetry_vdw_refined	0.131
r_nbd_other	0.125
r_xyhbond_nbd_refined	0.1
r_chiral_restr	0.08
r_nbtor_other	0.074
r_symmetry_hbond_refined	0.062
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1211
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing