4LY3 | pdb_00004ly3

Crystal structure of WlaRD, a sugar 3N-formyl transferase in the presence of dTPD-Qui3N, dTDP-Qui3NFo, and THF

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4LXQ	pdb entry 4LXQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	11-15% PEG 8000, 200 mM NaCl, 5 mM TDP, 5 mM N-5-formyl-THF, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.003	α = 90
b = 65.552	β = 109.83
c = 134.501	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	Bruker Platinum 135	mirrors	2013-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	92.8	0.05	0.05	15.9	3.6	58443	58443

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	pdb entry 4LXQ	1.9	50	58443	55503	2940	91.9	0.17999	0.17758	0.19	0.22617	0.23	RANDOM	18.94

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]
0.32		-0.06	0.82		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.692
r_dihedral_angle_3_deg	13.626
r_dihedral_angle_4_deg	13.25
r_dihedral_angle_1_deg	7.464
r_angle_refined_deg	1.99
r_angle_other_deg	0.881
r_chiral_restr	0.116
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4472
Nucleic Acid Atoms
Solvent Atoms	609
Heterogen Atoms	162

Software

Software
Software Name	Purpose
APEX	data collection
PHASER	phasing
REFMAC	refinement
APEX	data reduction