6SS2 | pdb_00006ss2

Structure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0021158

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SS4	6SS4, 6SRX
experimental model	PDB	6SRX	6SS4, 6SRX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Crystallisation condition: 2 M (NH4)2SO4 Seed condition (approx. final conc.) 20 mM MIB (malonate, imidazole, boric acid) 4% glycerol 2% PEG4000 9 mM NaNO3 9 mM Na2HPO4 9 mM (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.061	α = 90
b = 149.061	β = 90
c = 123.287	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	PIXEL	DECTRIS PILATUS 6M-F		2019-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.4	45.37	99.9	0.17	0.99	7	5.2		39908

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	100		1.72	0.36	1	5.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6SS4, 6SRX	2.4	45.368	39901	1976	99.88	0.255	0.2538	0.19	0.2842	0.22	48.54

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]
1.969			1.969		-3.938

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.509
r_dihedral_angle_3_deg	17.55
r_dihedral_angle_4_deg	12.136
r_dihedral_angle_1_deg	7.536
r_lrange_it	4.405
r_lrange_other	4.338
r_mcangle_it	1.704
r_mcangle_other	1.704
r_scangle_it	1.593
r_scangle_other	1.418
r_angle_refined_deg	1.413
r_scbond_it	1.393
r_angle_other_deg	1.137
r_scbond_other	1.122
r_mcbond_it	1.026
r_mcbond_other	1.023
r_nbd_other	0.212
r_symmetry_nbd_refined	0.199
r_nbd_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.18
r_symmetry_nbd_other	0.172
r_xyhbond_nbd_refined	0.166
r_nbtor_refined	0.156
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.054
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5680
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	207

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building