8JQ6

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

X-RAY DIFFRACTION

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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
2.33	47.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.934	α = 90
b = 140.057	β = 90
c = 147.47	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	1.71	49.16	100	0.148	0.154	0.042	0.998	12.6	13.2		200687

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	1.71	1.74		99.7	1.338	1.393	0.386	0.7		12.7

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	1.71	46.43	190503	10079	99.95	0.14203	0.13967	0.18702	RANDOM	19.501

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]
0.23			-0.48		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.736
r_dihedral_angle_4_deg	18.482
r_dihedral_angle_3_deg	13.87
r_dihedral_angle_1_deg	6.118
r_rigid_bond_restr	4.253
r_long_range_B_refined	2.681
r_long_range_B_other	2.612
r_scangle_other	2.206
r_mcangle_it	1.789
r_mcangle_other	1.789
r_scbond_it	1.706
r_scbond_other	1.706
r_mcbond_it	1.332
r_mcbond_other	1.329
r_angle_other_deg	1.325
r_angle_refined_deg	1.222
r_chiral_restr	0.06
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
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	13327
Nucleic Acid Atoms
Solvent Atoms	986
Heterogen Atoms	104

Software

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