8BRZ | pdb_00008brz

Room-temperature structure of Pedobacter heparinus N-acetylglucosamine 2-epimerase at 52 MPa helium gas pressure in a sapphire capillary

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	12.6 mg/ml protein in 20 mM sodium phosphate buffer pH 7.5 were mixed (4+2 ul) with 0.1 M sodium cacodylate buffer pH 5.0, 0.35 M sodium acetate and 26% PEG 8000. Crystals grew at room temperature in 5-7 days.

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.41	α = 90
b = 94.08	β = 102.63
c = 81.71	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	295	PIXEL	DECTRIS PILATUS3 X CdTe 2M		2020-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	0.477	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	41.28	96.35	0.2875	0.3072	0.1042	0.983	5.64	7.9		88642			17.71

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.761	82.55		1.751	1.892	0.6563	0.242	0.95	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	MOLECULAR REPLACEMENT	FREE R-VALUE	2GZ6	1.7	41.28	1.34	88072	1524	96.36	0.1579	0.1575	0.16	0.183	0.18	24.4

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	26.5443
f_angle_d	0.6866
f_chiral_restr	0.0403
f_bond_d	0.0039
f_plane_restr	0.0039

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6404
Nucleic Acid Atoms
Solvent Atoms	474
Heterogen Atoms	12

Software

Software
Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

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.