6WFV | pdb_00006wfv

The crystal structure of a collagen galactosylhydroxylysyl glucosyltransferase from human

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose
2	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose, crystal soaked in higher Mn and UDP-Glc prior to flash cooling.
3	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose. Crystal soaked in 1 M NaI prior to flash cooling

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.066	α = 90
b = 71.066	β = 90
c = 110.813	γ = 120

Symmetry
Space Group	P 32 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 PILATUS3 6M		2016-06-02	M	SINGLE WAVELENGTH
2	2	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2016-10-12	M	SINGLE WAVELENGTH
3	3	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2016-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1271	ALS	8.3.1
2	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1158	ALS	8.3.1
3	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.7136	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.7	41.18	99.7	0.117	0.12	0.999	19.67	17.521		36393			31.679

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.74	96.4		1.64	1.73	0.717	2.1	9.969

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	1.7	41.18	35211	1931	96.48	0.1528	0.1516	0.15	0.1722	0.17	34.1078

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	14.7149
f_angle_d	1.172
f_chiral_restr	0.0532
f_bond_d	0.0097
f_plane_restr	0.0065

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1892
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	79

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHELXD	phasing
SOLVE	phasing
RESOLVE	model building
SHELXE	model building
Coot	model building
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.