6ZRZ

Crystal structure of 5-dimethylallyl tryptophan synthase from Streptomyces coelicolor in complex with DMASPP and Trp

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5INJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	150 mM Bis-Tris 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.82	32.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.658	α = 90
b = 70.147	β = 92.722
c = 91.082	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 2M-F		2020-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00002	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.696	45.5	97	0.065	0.99	15.4	4.5		62994			32.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.696	1.8			1	0.59

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5INJ	1.696	45.49	60392	1812	96.948	0.182	0.1811	0.19	0.2189	0.22	28.515

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]
-0.008		-0.269	0.396		-0.361

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.805
r_dihedral_angle_4_deg	20.921
r_dihedral_angle_3_deg	14.104
r_dihedral_angle_1_deg	6.585
r_lrange_it	5.228
r_lrange_other	5.134
r_scangle_it	2.48
r_scangle_other	2.479
r_mcangle_it	2.155
r_mcangle_other	2.155
r_scbond_it	1.544
r_scbond_other	1.543
r_chiral_restr_other	1.463
r_angle_refined_deg	1.455
r_angle_other_deg	1.34
r_mcbond_it	1.275
r_mcbond_other	1.275
r_nbd_other	0.217
r_nbd_refined	0.199
r_symmetry_xyhbond_nbd_refined	0.196
r_symmetry_nbd_other	0.188
r_symmetry_nbd_refined	0.179
r_xyhbond_nbd_refined	0.166
r_nbtor_refined	0.158
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.061
r_xyhbond_nbd_other	0.03
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5269
Nucleic Acid Atoms
Solvent Atoms	412
Heterogen Atoms	58

Software

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