7NZP | pdb_00007nzp

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y0O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.5	291	200 mM ammonium acetate, 100 mM Bis-Tris pH 5.5, 25 % w/v PEG 3350, 15 mM fructose

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.958	α = 90
b = 86.647	β = 112.274
c = 53.837	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	100	PIXEL	DECTRIS EIGER2 XE 16M		2020-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.345	86.65	100	0.999	14.9	13.4		88231

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	1.345	1.37			0.333

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2y0o	1.345	49.819	88130	4293	99.906	0.185	0.1837	0.18	0.2126	0.21	34.936

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]
2.019		0.367	-1.609		-0.532

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.964
r_dihedral_angle_4_deg	18.687
r_dihedral_angle_3_deg	14.443
r_lrange_it	8.368
r_dihedral_angle_1_deg	6.583
r_scangle_it	5.666
r_mcangle_it	4.235
r_scbond_it	3.906
r_mcbond_it	2.912
r_angle_refined_deg	1.838
r_nbtor_refined	0.319
r_symmetry_xyhbond_nbd_refined	0.229
r_nbd_refined	0.215
r_symmetry_nbd_refined	0.211
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.107
r_ncsr_local_group_1	0.096
r_gen_planes_refined	0.011
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3001
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MoRDa	phasing