6Q92 | pdb_00006q92

Crystal structure of human Arginase-1 at pH 7.0 in complex with ABH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AEB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	Crystals were generated from 22 % PEG 1500, 0.2 M MIB buffer pH 4.0 (sodium malonate, imidazole and boric acid in a 2:3:3 molar ratio). Crystals were equilibrated to soaking solution (22 % PEG 1500, 0.2 M MMT buffer pH 7.0 (DL-malic acid, MES, Tris base in a 1:2:2 molar ratio). Subsequently, crystals were gradually soaked for 13 days in soaking solution containing 15 mM ABH.

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.38	α = 90
b = 90.38	β = 90
c = 69.254	γ = 120

Symmetry
Space Group	P 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 PILATUS3 2M	transfocator	2017-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.5	39.14	98.2	0.097	0.122	0.074	0.987	6.9	2.4		99464			13.91

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	96.4		0.608	0.796	0.508	0.293	1.8	2.1

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2AEB	1.5	39.14	95151	4304	98.14	0.13544	0.13483	0.12	0.14721	0.14	RANDOM	16.294

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]
0.52			0.52		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.942
r_dihedral_angle_4_deg	14.33
r_dihedral_angle_3_deg	12.365
r_dihedral_angle_1_deg	6.019
r_sphericity_bonded	4.619
r_long_range_B_refined	4.087
r_sphericity_free	3.713
r_long_range_B_other	3.645
r_scangle_other	1.551
r_mcangle_it	1.356
r_mcangle_other	1.356
r_angle_refined_deg	1.306
r_scbond_it	0.953
r_scbond_other	0.953
r_mcbond_it	0.798
r_mcbond_other	0.798
r_angle_other_deg	0.771
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4830
Nucleic Acid Atoms
Solvent Atoms	624
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing