8JQ5

Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with D-allulose

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DE5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	PEG550MME, MES

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.887	α = 90
b = 139.445	β = 90
c = 146.834	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS3 S 2M		2020-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	1.73	48.94	100	0.118	0.123	0.033	0.999	17.5	13.4		192191

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	1.73	1.76		100	1.414	1.469	0.396	0.722		13.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.73	46.23	182641	9442	99.99	0.14174	0.13936	0.18671	RANDOM	21.6

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]
0.08			-0.32		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.131
r_dihedral_angle_4_deg	18.686
r_dihedral_angle_3_deg	14.429
r_dihedral_angle_1_deg	6.27
r_rigid_bond_restr	4.796
r_long_range_B_refined	3.16
r_long_range_B_other	3.109
r_scangle_other	2.714
r_mcangle_other	2.303
r_mcangle_it	2.301
r_scbond_it	2.104
r_scbond_other	2.104
r_mcbond_it	1.737
r_mcbond_other	1.716
r_angle_other_deg	1.307
r_angle_refined_deg	1.262
r_chiral_restr	0.06
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13531
Nucleic Acid Atoms
Solvent Atoms	827
Heterogen Atoms	104

Software

Software
Software Name	Purpose
Aimless	data scaling
XDS	data reduction
REFMAC	refinement
MOLREP	phasing