7ZGN | pdb_00007zgn

Plant/insect N-glycan active PNGase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R4Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	10 mM Cobalt chloride hexahydrate, 100 mM Tris pH 8.5 and 10% w/v Polyvinylpyrrolidone K15

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.05	α = 90
b = 100.55	β = 90
c = 180.37	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M		2017-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97949	Diamond	I03

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	1.95	45.09	99.9	0.999	12.6	7.2		79080

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	1.95	1.99	99.6		0.517	1.7	7.2

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	NONE	4r4z	1.95	44.379	79007	3990	99.77	0.192	0.1892	0.2	0.2395	0.24	45.568

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]
0.568			-0.597		0.029

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.292
r_dihedral_angle_6_deg	16.837
r_dihedral_angle_3_deg	16.535
r_lrange_it	10.792
r_lrange_other	10.791
r_scangle_it	8.874
r_scangle_other	8.873
r_dihedral_angle_1_deg	8.089
r_mcangle_it	7.213
r_mcangle_other	7.213
r_scbond_it	6.365
r_scbond_other	6.365
r_mcbond_it	5.668
r_mcbond_other	5.667
r_angle_refined_deg	1.768
r_angle_other_deg	0.577
r_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.201
r_symmetry_nbd_other	0.2
r_nbd_other	0.189
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.173
r_symmetry_nbd_refined	0.151
r_ncsr_local_group_1	0.105
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.082
r_symmetry_xyhbond_nbd_other	0.034
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8305
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
MolProbity	model building
PHASER	phasing
Aimless	data scaling
pointless	data scaling
xia2	data reduction
XDS	data reduction