3E61 | pdb_00003e61

Crystal structure of a putative transcriptional repressor of ribose operon from Staphylococcus saprophyticus subsp. saprophyticus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	3M sodium formate, 275mM sodium thiocyanate, pH 7.0, Vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.146	α = 90
b = 106.634	β = 112.17
c = 68.183	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	MAR CCD 165 mm		2008-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	19.749	99.7	0.103	0.103	12.3	5.1	36225	36116			28.1

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	2.11	99.4		0.587	0.587	2.8	5.1	5227

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	SAD	THROUGHOUT	2	19.749	36225	36098	1842	99.65	0.214	0.212	0.21	0.259	0.26	RANDOM	39.625

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]
-1.78		0.03	1.62		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.528
r_dihedral_angle_4_deg	22.713
r_dihedral_angle_3_deg	16.631
r_dihedral_angle_1_deg	5.978
r_scangle_it	3.925
r_scbond_it	2.656
r_mcangle_it	1.65
r_angle_refined_deg	1.542
r_mcbond_it	1.012
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.528
r_dihedral_angle_4_deg	22.713
r_dihedral_angle_3_deg	16.631
r_dihedral_angle_1_deg	5.978
r_scangle_it	3.925
r_scbond_it	2.656
r_mcangle_it	1.65
r_angle_refined_deg	1.542
r_mcbond_it	1.012
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.298
r_symmetry_vdw_refined	0.277
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.111
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3691
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.