5XGX | pdb_00005xgx

Crystal structure of colwellia psychrerythraea strain 34H isoaspartyl dipeptidase E80Q mutant complexed with beta-isoaspartyl lysine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Bis-Tris propane pH 7.0 1 M ammonium citrate tribasic pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.878	α = 90
b = 107.878	β = 90
c = 155.879	γ = 90

Symmetry
Space Group	P 4 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2017-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.9796	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.33	50.01	97.1	31.8	6.8		36407

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.33	50.01	36407	1910	95.88	0.19177	0.18886	0.2	0.24636	0.25	RANDOM	39.708

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]
0.72			0.72		-1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.197
r_dihedral_angle_4_deg	24.997
r_dihedral_angle_3_deg	15.283
r_long_range_B_refined	8.272
r_long_range_B_other	8.245
r_dihedral_angle_1_deg	7.503
r_scangle_other	6.071
r_mcangle_other	4.634
r_mcangle_it	4.633
r_scbond_it	4.038
r_scbond_other	4.038
r_mcbond_it	3.17
r_mcbond_other	3.168
r_angle_refined_deg	1.84
r_angle_other_deg	1.075
r_chiral_restr	0.111
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5780
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling