3D5P | pdb_00003d5p

CRYSTAL STRUCTURE OF A PUTATIVE GLUCAN SYNTHESIS REGULATOR OF SMI1/KNR4 FAMILY (BF1740) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 1.45 A RESOLUTION

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277	15.0000% Glycerol, 0.1700M NH4OAc, 25.5000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.058	α = 90
b = 69.508	β = 90
c = 75.093	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 325 mm CCD	Flat mirror (vertical focusing)	2008-04-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97916,0.97852	SSRL	BL11-1

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	1.45	29.683	98	0.065	0.065	7.6	3.7		52450			15.17

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	1.45	1.49	83		0.558	0.558	1.4	3.3	3206

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	1.45	29.683	52409	2676	97.72	0.157	0.156	0.17	0.175	0.18	RANDOM	13.475

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]
0.11			-0.3		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.071
r_dihedral_angle_4_deg	20.154
r_dihedral_angle_3_deg	14.591
r_dihedral_angle_1_deg	5.803
r_scangle_it	2.718
r_mcangle_it	2.25
r_scbond_it	1.847
r_angle_refined_deg	1.677
r_angle_other_deg	1.418
r_mcbond_it	1.369

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.071
r_dihedral_angle_4_deg	20.154
r_dihedral_angle_3_deg	14.591
r_dihedral_angle_1_deg	5.803
r_scangle_it	2.718
r_mcangle_it	2.25
r_scbond_it	1.847
r_angle_refined_deg	1.677
r_angle_other_deg	1.418
r_mcbond_it	1.369
r_mcbond_other	0.375
r_chiral_restr	0.107
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2138
Nucleic Acid Atoms
Solvent Atoms	335
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	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.