2Y75 | pdb_00002y75

The Structure of CymR (YrzC) the Global Cysteine Regulator of B. subtilis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	OPTIMIZATION OF INITIAL HITS WAS PURSUED MANUALLY IN LINBRO PLATES WITH A HANGING DROP SETUP. THE BEST CRYSTALS WERE OBTAINED BY MIXING 1.5 UL OF NATIVE CYMR PROTEIN OR SELENOMETHIONINE LABELED PROTEIN AT 14 MG/ML WITH 1.5 UL OF THE RESERVOIR SOLUTION CONTAINING 1.6 M AMMONIUM SULPHATE AND 0.1 M TRIS-HCL PH 8.5 AT 18 C DEGREES. THE CRYSTALS APPEARED WITHIN ONE WEEK AND HAD DIMENSIONS OF UP TO 0.1 MM X 0.1 MM X 0.2 MM. A SINGLE CRYSTAL OF THE CYMR PROTEIN WAS FLASH-FROZEN IN LIQUID NITROGEN USING A MIXTURE OF 50% PARATONE AND 50% PARAFFIN OIL AS CRYOPROTECTANT.

Crystal Properties
Matthews coefficient	Solvent content
2.96	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.7	α = 90
b = 103.7	β = 90
c = 106.53	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	ADSC QUANTUM 315r		2008-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	17.84	99	0.06	14.42	3.64		73831		-3	36.49

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	2.05	99.6		0.74	2.03	3.68

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	SAD	THROUGHOUT	NONE	2	17.84	73692	3715		0.1884	0.1871	0.1955	0.2136	0.2259	RANDOM	41.6

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]
0.5589			0.1613		-0.7201

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.51
t_omega_torsion	2.93
t_angle_deg	1.09
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5878
Nucleic Acid Atoms
Solvent Atoms	870
Heterogen Atoms	83

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling