6TUL | pdb_00006tul

Structure of the arginase-2-inhibitory human antigen-binding fragment Fab C0021177

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SRV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	100 mM MMT (D/L-malic acid, MES, tris) 25% PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.537	α = 90
b = 69.244	β = 90
c = 106.517	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	PIXEL	DECTRIS PILATUS 6M-F		2019-09-25	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	2.25	47.83	100	0.18	1	8.4	12.8		19456

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	2.25	2.32	99.9		4.04	0.36	0.7	13.3

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	6SRV	2.25	47.505	19407	994	99.943	0.252	0.2482	0.25	0.3176	0.31	62.164

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]
4.928			-3.131		-1.796

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.373
r_dihedral_angle_3_deg	16.771
r_dihedral_angle_4_deg	9.27
r_dihedral_angle_1_deg	6.759
r_lrange_it	3.153
r_lrange_other	3.153
r_mcangle_it	1.236
r_mcangle_other	1.236
r_angle_refined_deg	1.218
r_angle_other_deg	1.039
r_scangle_it	0.734
r_scangle_other	0.734
r_mcbond_it	0.667
r_mcbond_other	0.667
r_scbond_other	0.376
r_scbond_it	0.375
r_nbd_other	0.186
r_nbd_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.163
r_symmetry_nbd_other	0.157
r_nbtor_refined	0.15
r_symmetry_nbd_refined	0.123
r_xyhbond_nbd_refined	0.108
r_symmetry_nbtor_other	0.068
r_chiral_restr	0.031
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3201
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	83

Software

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