9H88 | pdb_00009h88

Crystal structure of LmrR variant V15aY-RNYW with Val15 replaced by 3-aminotyrosine and evolved as Friedel-Crafts alkylase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6I8N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	The protein solution contained 16 mg/ml protein in 20 mM HEPES, pH 7, 280 mM NaCl. The reservoir solution contained 0.2 M Na-citrate, 0.1 M Bis-Tris propane, pH 8.5, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
	24.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.7	α = 90
b = 58.533	β = 90
c = 74	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 PILATUS 6M		2024-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	ESRF	MASSIF-1

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	1.2	74	99.8	0.062	0.065	0.018	1	17.4	12.3		62694

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	1.2	1.22		96	2.211	2.36	0.803	0.409		8.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.2	45.95	59446	3173	99.77	0.17618	0.17425	0.1744	0.21268	0.213	RANDOM	20.756

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]
-1.88			4.21		-2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	13.376
r_dihedral_angle_3_deg	13.101
r_long_range_B_other	12.857
r_scangle_other	10.134
r_dihedral_angle_2_deg	7.213
r_scbond_it	7.062
r_scbond_other	7.036
r_mcangle_other	6.602
r_mcangle_it	6.593
r_rigid_bond_restr	6.078
r_dihedral_angle_1_deg	4.768
r_mcbond_it	4.532
r_mcbond_other	4.532
r_angle_refined_deg	1.721
r_angle_other_deg	0.617
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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	1831
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	12

Software

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