9FDD | pdb_00009fdd

The crystal structure of full length tetramer CysB from Klebsiella aerogenes in complex with N-acetylserine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AL3	c

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	12-17% PEG 8000, 0.2 M sodium tartrate, 0.1 M Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.436	α = 90
b = 187.436	β = 90
c = 224.662	γ = 120

Symmetry
Space Group	H 3

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		1998-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.87	SRS	PX9.6

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	2.8	41.462	99.4	0.089	5.9	5.7		72415			35.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.8	41.462	72368	3626	99.916	0.183	0.18	0.19	0.2456	0.24	45.469

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]
0.862	0.431		0.862		-2.797

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.357
r_dihedral_angle_6_deg	14.245
r_lrange_it	9.309
r_lrange_other	9.308
r_dihedral_angle_2_deg	7.41
r_dihedral_angle_1_deg	7.234
r_scangle_it	6.563
r_scangle_other	6.563
r_mcangle_it	6.35
r_mcangle_other	6.349
r_scbond_it	4.046
r_scbond_other	4.046
r_mcbond_it	3.98
r_mcbond_other	3.98
r_angle_refined_deg	1.753
r_angle_other_deg	0.587
r_symmetry_nbd_refined	0.224
r_nbd_refined	0.223
r_symmetry_nbd_other	0.207
r_nbd_other	0.196
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.141
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20288
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
HKL-3000	data reduction
Aimless	data scaling
MOLREP	phasing