6ZRX | pdb_00006zrx

Crystal structure of 6-dimethylallyltryptophan synthase from Micromonospora olivasterospora 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		277	200 mM Calcium acetate, 26% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.021	α = 90
b = 98.471	β = 107.487
c = 89.185	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 EIGER X 16M		2017-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00001	SLS	X06SA

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	1.69	39.673	98.5	0.09	0.99	11.3	4		143483			30.3

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	1.69	1.79	98.5		0.68	0.82	2.1	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	1.7	39.673	139303	1671	98.729	0.202	0.2021	0.21	0.2302	0.23	23.708

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]
0.944		-0.324	0.041		-0.652

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.02
r_dihedral_angle_4_deg	16.905
r_dihedral_angle_3_deg	12.828
r_dihedral_angle_1_deg	5.971
r_lrange_it	4.173
r_lrange_other	4.156
r_mcangle_it	2.011
r_mcangle_other	2.011
r_scangle_it	1.982
r_scangle_other	1.982
r_angle_refined_deg	1.246
r_angle_other_deg	1.213
r_scbond_it	1.203
r_scbond_other	1.202
r_mcbond_it	1.174
r_mcbond_other	1.174
r_nbd_refined	0.185
r_nbd_other	0.176
r_symmetry_nbd_refined	0.172
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.151
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_other	0.085
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.053
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10771
Nucleic Acid Atoms
Solvent Atoms	971
Heterogen Atoms	170

Software

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