3FWR | pdb_00003fwr

Crystal Structure of the CBS domains from the Bacillus subtilis CcpN repressor complexed with ADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FV6	PDB ENTRY 3FV6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	17% PEG 2000 MME, 0.1M HEPES, 8mg/ml Protein; Drops 1+1 microliter, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.273	α = 90
b = 103.047	β = 90
c = 98.342	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	78	CCD	ADSC QUANTUM 315r		2006-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.93300	ESRF	ID23-1

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	2.45	98.53	92.9	0.103	0.095	19.5	6.8		9555			41.041

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	2.45	2.58	92.9		0.545	0.477	2.6	4	4024

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3FV6	2.45	45.64	9437	284	92.85	0.20219	0.19983	0.21	0.28073	0.29	RANDOM	23.022

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]
-0.25			0.24		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.813
r_dihedral_angle_4_deg	21.434
r_dihedral_angle_3_deg	18.239
r_dihedral_angle_1_deg	8.195
r_scangle_it	3.135
r_scbond_it	1.917
r_angle_refined_deg	1.872
r_mcangle_it	1.114
r_mcbond_it	0.602
r_chiral_restr	0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.813
r_dihedral_angle_4_deg	21.434
r_dihedral_angle_3_deg	18.239
r_dihedral_angle_1_deg	8.195
r_scangle_it	3.135
r_scbond_it	1.917
r_angle_refined_deg	1.872
r_mcangle_it	1.114
r_mcbond_it	0.602
r_chiral_restr	0.115
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2285
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	54

Software

Software
Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.