6QAF | pdb_00006qaf

Crystal structure of human Arginase-1 at pH 9.0 in complex with CB-1158/INCB001158

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q9P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	Crystals were generated from 22.5 % 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 (22.5 % PEG 1500, 0.2 M MMT buffer pH 9.0 (DL-malic acid, MES, Tris base in a 1:2:2 molar ratio). Subsequently, crystals were gradually soaked for 4 days in soaking solution containing 15 mM compound 3.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.13	α = 90
b = 90.13	β = 90
c = 69.111	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	2017-12-14	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	1.61	51.74	96.9	0.058	0.076	0.049	0.996	6.9	2		79090			20.01

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	1.61	1.64	96		0.658	0.868	0.561	0.368		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	6Q9P	1.61	51.74	74978	4105	96.85	0.149	0.14744	0.13	0.177	0.15	RANDOM	24.684

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]
3.48			3.48		-6.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.348
r_dihedral_angle_4_deg	14.635
r_dihedral_angle_3_deg	12.91
r_dihedral_angle_1_deg	6.164
r_sphericity_bonded	5.325
r_sphericity_free	4.94
r_long_range_B_refined	3.683
r_long_range_B_other	3.657
r_scangle_other	1.999
r_mcangle_it	1.991
r_mcangle_other	1.991
r_angle_refined_deg	1.356
r_mcbond_it	1.277
r_mcbond_other	1.277
r_scbond_it	1.274
r_scbond_other	1.266
r_angle_other_deg	0.806
r_chiral_restr	0.077
r_bond_refined_d	0.009
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	376
Heterogen Atoms	48

Software

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