4CJ8 | pdb_00004cj8

monoclinic crystal form of Bogt6a E192Q in complex with UDP-GalNAc, UDP and GalNAc

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		0.2M LI2SO4 0.1M BIS TRIS, PH 5.5 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.5	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 176.69	α = 90
b = 79.74	β = 95.23
c = 179.08	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	289.15	CCD	ADSC CCD	MIRRORS	2012-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	3.5	87.98	98	0.13	7.4	2.7		61949		7.4

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	3.5	3.59	99		0.7	2.1	7.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	PDB ENTRY 4CJB	3.5	87.977	1.34	61938	3254	97.73	0.2266	0.2253	0.2366	0.2494	0.2617

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.518
f_angle_d	0.529
f_chiral_restr	0.023
f_plane_restr	0.003
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32187
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	683

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing