6SS4 | pdb_00006ss4

Structure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0021181

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HZE	4HZE,6SS0
experimental model	PDB	6SS0	4HZE,6SS0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	100 mM MMT pH 5.0 (malic acid, MES, tris) 20% glycerol 10% PEG4000 15 mM NaNO3 15 mM Na2HPO4 15 mM (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
4.25	71.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.38	α = 90
b = 150.38	β = 90
c = 110.74	γ = 120

Symmetry
Space Group	P 3 2 1

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		2018-05-12	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	2.9	44.98	100	0.35	1	11	20.2		32384

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	2.9	3.06	100		5.19	0.32	0.7	20.8

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	4HZE,6SS0	2.9	44.98	32381	1602	99.975	0.268	0.2655	0.19	0.3181	0.24	79.623

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]
-14.109			-14.109		28.219

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.323
r_dihedral_angle_4_deg	23.645
r_dihedral_angle_3_deg	22.781
r_lrange_it	8.432
r_lrange_other	8.432
r_dihedral_angle_1_deg	8.237
r_mcangle_it	3.846
r_mcangle_other	3.845
r_scangle_it	3.347
r_scangle_other	3.267
r_scbond_it	2.396
r_mcbond_it	2.386
r_mcbond_other	2.384
r_scbond_other	2.341
r_angle_refined_deg	2.012
r_angle_other_deg	1.379
r_symmetry_xyhbond_nbd_refined	0.338
r_symmetry_nbd_refined	0.274
r_nbd_other	0.27
r_symmetry_nbd_other	0.225
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.218
r_nbtor_refined	0.185
r_symmetry_nbtor_other	0.09
r_symmetry_xyhbond_nbd_other	0.081
r_chiral_restr	0.08
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5619
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	7

Software

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