5LX0

Cys-Gly dipeptidase GliJ (space group P3221)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	0.1 M MES pH 6.0, 5 % isopropanol

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.01	α = 90
b = 100.01	β = 90
c = 107.15	γ = 120

Symmetry
Space Group	P 32 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 EIGER X 16M		2016-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.738	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	45	99.5	0.062	18.9	7.6		46680

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.5	96.1		0.239	3.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ITQ	2.4	15	23274	1225	99.24	0.17269	0.17147	0.1949	RANDOM	53.347

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]
0.51	0.26		0.51		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.22
r_sphericity_free	24.232
r_dihedral_angle_3_deg	13.762
r_sphericity_bonded	12.632
r_dihedral_angle_4_deg	12.139
r_dihedral_angle_1_deg	5.66
r_long_range_B_refined	2.284
r_long_range_B_other	2.011
r_mcangle_it	1.481
r_mcangle_other	1.481
r_scangle_other	1.307
r_mcbond_it	1.103
r_mcbond_other	1.102
r_scbond_other	1.092
r_scbond_it	1.091
r_angle_refined_deg	1.078
r_angle_other_deg	0.896
r_rigid_bond_restr	0.721
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3007
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	2

Software

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