7NZO | pdb_00007nzo

D-lyxose isomerasefrom the hyperthermophilic archaeon Thermofilum sp

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	7	293	150 mM Potassium bromide, 30% w/v PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.77	α = 90
b = 86.91	β = 112.93
c = 54.03	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		2021-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	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	1.67	39.26	92.2	0.999	19.4	6.2		43436

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	1.67	1.7			0.326

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	1.67	39.252	43408	2053	92.132	0.181	0.1792	0.18	0.2107	0.21	41.016

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]
2.535		0.653	-2.531		-0.409

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.862
r_dihedral_angle_4_deg	16.665
r_dihedral_angle_3_deg	13.972
r_lrange_it	8.334
r_scangle_it	6.553
r_dihedral_angle_1_deg	6.396
r_scbond_it	4.8
r_mcangle_it	4.241
r_mcbond_it	3.34
r_angle_refined_deg	1.612
r_nbtor_refined	0.318
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.194
r_symmetry_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.114
r_ncsr_local_group_1	0.071
r_gen_planes_refined	0.01
r_bond_refined_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2907
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing