1K2X | pdb_00001k2x

Crystal structure of putative asparaginase encoded by Escherichia coli ybiK gene

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GAW	PDB ENTRY 2GAW, polyalanine model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	PEG 4000, PEG 400, magnesium chloride, Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.296	α = 90
b = 77.624	β = 90
c = 148.152	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	IMAGE PLATE	MARRESEARCH	Toroidal mirror	1999-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	1.0442	EMBL/DESY, HAMBURG	X31

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	1.65	20		0.075	16.8	5.6	70249	70249		-3

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	1.65	1.68	89.9		0.476	2.5	5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 2GAW, polyalanine model	1.65	19.5	69077	69077	1064	99.52	0.16349	0.16295	0.18	0.19836	0.21	RANDOM	10.18

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]
-0.09			0.51		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.832
r_dihedral_angle_1_deg	3.992
r_scangle_it	2.961
r_scbond_it	1.763
r_angle_refined_deg	1.411
r_angle_other_deg	1.105
r_mcangle_it	1.011
r_nbtor_other	0.821
r_mcbond_it	0.529
r_nbd_refined	0.3
r_symmetry_vdw_other	0.223
r_nbd_other	0.212
r_symmetry_hbond_refined	0.187
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_other	0.162
r_xyhbond_nbd_refined	0.149
r_metal_ion_refined	0.099
r_symmetry_hbond_other	0.08
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4240
Nucleic Acid Atoms
Solvent Atoms	575
Heterogen Atoms	11

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement