4KC4 | pdb_00004kc4

Structure of the blood group glycosyltransferase AAglyB in complex with a pyridine inhibitor as a neutral pyrophosphate surrogate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IOI	PDB entry 3IOI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	13% or 15% PEG 3350, 50 mM or 150 mM ammonium sulfate and 50 mM MOPS pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.93	α = 90
b = 149.87	β = 90
c = 80.1	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	MARMOSAIC 225 mm CCD		2012-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	1.6	50	99.9	0.093	11.92		42400	42400	-3	-3	24.054

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	1.6	1.8	100		0.643	2.87

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 3IOI	1.6	36.33	42400	42400	1272	99.87	0.1469	0.1456	0.1456	0.1919	0.1915	RANDOM	20.1065

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]
-1.21			1.55		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	42.138
r_dihedral_angle_2_deg	32.416
r_dihedral_angle_4_deg	14.079
r_sphericity_bonded	13.835
r_dihedral_angle_3_deg	12.123
r_dihedral_angle_1_deg	5.625
r_scbond_it	1.557
r_mcangle_it	1.408
r_rigid_bond_restr	1.183
r_angle_refined_deg	1.156
r_mcbond_it	1.116
r_chiral_restr	0.086
r_bond_refined_d	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2356
Nucleic Acid Atoms
Solvent Atoms	431
Heterogen Atoms	69

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction