6ZS0 | pdb_00006zs0

Crystal structure of 5-dimethylallyltryptophan synthase from Streptomyces coelicolor

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 23% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.88	α = 90
b = 70.454	β = 92.946
c = 91.145	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	1.5	45.5	97.7	0.01	0.99	15.4	4.6		88635			27.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59			0.61	1.4

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	1.5	41.055	88630	1773	97.692	0.19	0.1891	0.2	0.2199	0.23	23.913

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]
0.064		0.016	0.478		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.075
r_dihedral_angle_4_deg	17.52
r_dihedral_angle_3_deg	13.789
r_dihedral_angle_1_deg	6.543
r_lrange_it	5.215
r_lrange_other	5.151
r_scangle_it	1.877
r_scangle_other	1.876
r_mcangle_it	1.747
r_mcangle_other	1.747
r_angle_refined_deg	1.425
r_angle_other_deg	1.385
r_scbond_it	1.119
r_scbond_other	1.119
r_mcbond_it	1.005
r_mcbond_other	1.005
r_symmetry_nbd_refined	0.314
r_nbd_other	0.249
r_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.07
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5227
Nucleic Acid Atoms
Solvent Atoms	524
Heterogen Atoms	14

Software

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