6UOF | pdb_00006uof

1.2 Angstrom Resolution Crystal Structure of CBS Domains of Transcriptional Regulator from Streptococcus pneumoniae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	Protein: 7.12 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3. Screen: Classics II (H1), 0.2M Magnesium chloride, 0.1M TRIS pH 8.5, 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.03	34.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.313	α = 90
b = 42.872	β = 90
c = 89.098	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 300 mm CCD	C(111)	2019-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.2	30	100	0.078	0.078	0.085	0.033	23.7	6.8		33475		-3	11.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	100		0.781	0.781	0.845	0.32	0.901	3.1	6.9

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	SAD	THROUGHOUT	1.2	26.11	31651	1724	99.62	0.1675	0.1665	0.1682	0.1861	0.187	RANDOM	16.808

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]
-0.38			0.24		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.69
r_dihedral_angle_3_deg	9.951
r_rigid_bond_restr	8.201
r_dihedral_angle_4_deg	7.974
r_dihedral_angle_1_deg	4.525
r_angle_refined_deg	1.578
r_angle_other_deg	0.45
r_chiral_restr	0.074
r_gen_planes_refined	0.053
r_gen_planes_other	0.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.69
r_dihedral_angle_3_deg	9.951
r_rigid_bond_restr	8.201
r_dihedral_angle_4_deg	7.974
r_dihedral_angle_1_deg	4.525
r_angle_refined_deg	1.578
r_angle_other_deg	0.45
r_chiral_restr	0.074
r_gen_planes_refined	0.053
r_gen_planes_other	0.048
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	949
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

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.