6XT5 | pdb_00006xt5

Jack bean asparaginyl endopeptidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NIJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	HEPES, PEG 20,000, EDTA disodium salt dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.989	α = 90
b = 88.882	β = 111.722
c = 109.848	γ = 90

Symmetry
Space Group	I 1 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		2018-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.984	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.69	46.33	98.8	0.997	9.6	3.4		26353

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.69	2.82			0.662

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	5NIJ	2.69	45.611	26351	1323	98.737	0.2	0.1958	0.2	0.2683	0.27	69.426

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]
-5.007		-1.323	1.247		3.654

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.15
r_dihedral_angle_3_deg	18.136
r_dihedral_angle_4_deg	11.748
r_lrange_it	8.187
r_lrange_other	8.186
r_dihedral_angle_1_deg	6.955
r_mcangle_it	5.847
r_mcangle_other	5.846
r_scangle_it	5.466
r_scangle_other	5.465
r_mcbond_it	3.751
r_mcbond_other	3.751
r_scbond_it	3.443
r_scbond_other	3.443
r_angle_refined_deg	1.355
r_angle_other_deg	1.126
r_nbd_other	0.257
r_nbd_refined	0.203
r_symmetry_nbd_other	0.176
r_symmetry_nbd_refined	0.172
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.081
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.051
r_symmetry_xyhbond_nbd_other	0.007
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6750
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Coot	model building
Aimless	data scaling