3CTP

Crystal structure of periplasmic binding protein/LacI transcriptional regulator from Alkaliphilus metalliredigens QYMF complexed with D-xylulofuranose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.1M Hepes pH 7.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.172	α = 90
b = 61.903	β = 104.81
c = 74.362	γ = 90

Symmetry
Space Group	P 1 21 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		2008-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97980	APS	31-ID

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	1.41	50	96.6	0.076	7.8	3.5		206130

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.41	1.46	72.2			1.8	15467

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	SAD	THROUGHOUT	1.41	9.99	102645	5140	94.93	0.183	0.182	0.207	RANDOM	17.288

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.819
r_dihedral_angle_3_deg	12.906
r_dihedral_angle_4_deg	11.265
r_scbond_it	6.33
r_dihedral_angle_1_deg	6.132
r_scangle_it	4.834
r_mcangle_it	3.736
r_angle_refined_deg	1.51
r_mcbond_it	1.347
r_chiral_restr	0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.819
r_dihedral_angle_3_deg	12.906
r_dihedral_angle_4_deg	11.265
r_scbond_it	6.33
r_dihedral_angle_1_deg	6.132
r_scangle_it	4.834
r_mcangle_it	3.736
r_angle_refined_deg	1.51
r_mcbond_it	1.347
r_chiral_restr	0.11
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4254
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms	22

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
SHELXD	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.