2JK0 | pdb_00002jk0

Structural and functional insights into Erwinia carotovora L- asparaginase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HG1	PDB ENTRY 1HG1

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.29	45.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.65	α = 90
b = 135.63	β = 90
c = 250.1	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	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	2.5	20	95.8	0.08	14	4.2		83599		-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	2.5	2.6	78		0.44	3.2	3.2

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1HG1	2.5	20	79398	4197	96.1	0.192	0.188	0.19	0.266	RANDOM	34.63

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]
0.13			-1.57		1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.788
r_dihedral_angle_4_deg	18.211
r_dihedral_angle_3_deg	18.201
r_dihedral_angle_1_deg	5.952
r_scangle_it	1.572
r_angle_refined_deg	1.292
r_scbond_it	0.975
r_mcangle_it	0.589
r_mcbond_it	0.333
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.291
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18719
Nucleic Acid Atoms
Solvent Atoms	708
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing