5LOE | pdb_00005loe

Structure of full length Cody from Bacillus subtilis in complex with Ile

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B18	2B18, 2B0L
experimental model	PDB	2B0L	2B18, 2B0L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	15% PEG5000, 0.1M HEPES pH 7.5, 5% tacsimate, 20mM Ile

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.69	α = 90
b = 158.877	β = 90
c = 55.412	γ = 90

Symmetry
Space Group	P 21 21 2

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	ADSC QUANTUM 4		2006-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	0.98000	SRS	PX10.1

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	3	50	92.5	0.065	25.3	5		22830

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11	47.3		0.654	0.96	2

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	2B18, 2B0L	3	45.45	21606	1164	92.44	0.21693	0.21225	0.21	0.30162	0.3	RANDOM	110.383

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]
-0.66			2.04		-1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.218
r_long_range_B_other	20.482
r_long_range_B_refined	20.481
r_dihedral_angle_3_deg	19.774
r_dihedral_angle_4_deg	17.254
r_scangle_other	15.89
r_mcangle_it	13.526
r_mcangle_other	13.525
r_scbond_it	10.933
r_scbond_other	10.915
r_mcbond_it	9.359
r_mcbond_other	9.342
r_dihedral_angle_1_deg	6.881
r_angle_refined_deg	1.647
r_angle_other_deg	1.078
r_chiral_restr	0.108
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8068
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing