7NZQ

D-lyxose isomerase from the hyperthermophilic archaeon Thermofilum sp complexed with D-mannose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6	291	100 mM SPG ph 6.0, 25% w/v PEG 1500, 40 mM D-mannose

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.909	α = 90
b = 121.013	β = 90
c = 70.537	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	PIXEL	DECTRIS EIGER2 XE 16M		2019-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.57	37.692	99.9	0.997	6.6	5.2		29074

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.57	1.6			0.277

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2y0o	1.57	37.692	29036	1439	99.852	0.178	0.1755	0.2176	25.025

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]
0.497			-0.034		-0.463

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.469
r_dihedral_angle_4_deg	16.376
r_dihedral_angle_3_deg	15.136
r_dihedral_angle_1_deg	6.74
r_lrange_it	6.582
r_scangle_it	4.155
r_scbond_it	3.003
r_mcangle_it	2.648
r_mcbond_it	1.882
r_angle_refined_deg	1.736

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.469
r_dihedral_angle_4_deg	16.376
r_dihedral_angle_3_deg	15.136
r_dihedral_angle_1_deg	6.74
r_lrange_it	6.582
r_scangle_it	4.155
r_scbond_it	3.003
r_mcangle_it	2.648
r_mcbond_it	1.882
r_angle_refined_deg	1.736
r_nbtor_refined	0.319
r_symmetry_nbd_refined	0.262
r_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.114
r_gen_planes_refined	0.01
r_bond_refined_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1464
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MoRDa	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 R01GM133198.