8JQ3

Crystal structure of L-rhamnose isomerase from Lactobacillus rhamnosus

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	PEG 550MME, MES

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.7	α = 90
b = 139.94	β = 90
c = 147.31	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)	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	1.9	50	100	0.086	0.08900000000000001	0.9990000000000001	22.94	13.5		146232

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95			0.6890000000000001	0.715	0.892

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	1.9	44.51	138900	7237	99.98	0.16264	0.15975	0.2176	RANDOM	25.671

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]
-0.21			-0.35		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.755
r_dihedral_angle_4_deg	19.592
r_dihedral_angle_3_deg	15.304
r_rigid_bond_restr	6.584
r_dihedral_angle_1_deg	5.975
r_long_range_B_refined	3.735
r_long_range_B_other	3.699
r_scangle_other	2.578
r_mcangle_it	2.443
r_mcangle_other	2.443
r_scbond_it	1.989
r_scbond_other	1.989
r_mcbond_it	1.811
r_mcbond_other	1.81
r_angle_other_deg	1.246
r_angle_refined_deg	1.183
r_chiral_restr	0.054
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	13367
Nucleic Acid Atoms
Solvent Atoms	741
Heterogen Atoms	8

Software

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