2YK4 | pdb_00002yk4

Structure of Neisseria LOS-specific sialyltransferase (NST).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YK5	PDB ENTRY 2YK5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.4		PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION METHODS USING DROPS OF PROTEIN MIXED WITH AN EQUAL VOLUME OF PRECIPITANT: 100 MM SODIUM ACETATE (PH 4.2 - 4.4) 1.7 M DI-AMMONIUM SULFATE.

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.565	α = 90
b = 124.735	β = 90
c = 41.866	γ = 90

Symmetry
Space Group	P 21 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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2		ALS	8.2.2

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	1.94	71.07	100	0.01	35.5	8.8		34365		2

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	1.94	1.97	99.9		0.05	3.22	8.5

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	PDB ENTRY 2YK5	1.94	71.07	32604	1735	99.92	0.19639	0.19499	0.2	0.22274	0.22	RANDOM	32.485

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]
-1.39			0.23		1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.987
r_dihedral_angle_4_deg	18.939
r_dihedral_angle_3_deg	16.014
r_dihedral_angle_1_deg	7.56
r_scangle_it	3.953
r_scbond_it	2.576
r_mcangle_it	1.82
r_angle_refined_deg	1.619
r_mcbond_it	1.036
r_chiral_restr	0.106
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2642
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing