6YMN

Crystal structure of the Diels Alderase AbmU from Streptomyces koyangensis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293.15	0.2 M Na acetate, 0.1 M Na cacodylate, 32% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.128	α = 90
b = 64.998	β = 93.813
c = 97.865	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 EIGER2 XE 16M		2019-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9197	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	2.05	56.44	99.8	0.178	0.043	0.998	12.25	18.8		52059

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	97.4		1.502	0.681

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.05	56.44	52035	2616	99.585	0.192	0.1889	0.2427	39.17

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]
-2.298		-0.627	0.846		1.522

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.553
r_dihedral_angle_4_deg	20.377
r_dihedral_angle_3_deg	15.831
r_lrange_it	7.717
r_lrange_other	7.625
r_dihedral_angle_1_deg	7.438
r_scangle_it	4.933
r_scangle_other	4.933
r_mcangle_it	4.553
r_mcangle_other	4.553
r_scbond_it	3.241
r_scbond_other	3.241
r_mcbond_it	2.996
r_mcbond_other	2.996
r_angle_other_deg	2.361
r_angle_refined_deg	1.638
r_symmetry_xyhbond_nbd_other	0.593
r_symmetry_nbd_other	0.228
r_symmetry_xyhbond_nbd_refined	0.213
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.196
r_nbd_other	0.195
r_nbtor_refined	0.164
r_symmetry_nbd_refined	0.161
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.075
r_bond_other_d	0.035
r_gen_planes_other	0.01
r_bond_refined_d	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6228
Nucleic Acid Atoms
Solvent Atoms	485
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data scaling
CRANK2	phasing