4LXY | pdb_00004lxy

Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTDP and 10-N-Formyl-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
3.14	60.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.337	α = 90
b = 65.858	β = 109.88
c = 134.6	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	2013-05-10	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	1.64	50	96.2	0.058	0.058	14.6	4	93525	93525

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.74	86.6		0.364	0.364	2.2	2.2	13710

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 (All)	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	1.64	48.21	93525	88820	4704	96.12	0.191	0.19095	0.18911	0.2	0.22564	0.23	RANDOM	18.836

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]
0.15		-0.29	1.22		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.809
r_dihedral_angle_4_deg	14.107
r_dihedral_angle_3_deg	13.723
r_dihedral_angle_1_deg	7.817
r_angle_refined_deg	2.078
r_angle_other_deg	0.908
r_chiral_restr	0.131
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d
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	4489
Nucleic Acid Atoms
Solvent Atoms	795
Heterogen Atoms	144

Software

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