8OF7 | pdb_00008of7

Cyc15 Diels Alderase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	100 mM glutamate monohydrate, 100 mM DL-alanine, 100 mM glycine, 100 mM DL-lysine monohydrochloride, 100 mM DL-serine, 100 mM imidazole, 100 mM MES monohydrate (acid), 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.14	α = 90
b = 65.14	β = 90
c = 180.14	γ = 90

Symmetry
Space Group	P 41 21 2

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		2022-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.66	46.1	100	0.101	0.9996	22.7	77.2		46918

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	1.66	1.69	99.65		0.299

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 (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	1.66	46.1	44470	2349	99.91	0.18877	0.18737	0.2	0.21497	0.2	RANDOM	60.267

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]
3.22			3.22		-6.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.084
r_long_range_B_other	10.589
r_long_range_B_refined	10.583
r_scangle_other	8.136
r_dihedral_angle_2_deg	7.714
r_dihedral_angle_1_deg	7.119
r_scbond_it	5.772
r_scbond_other	5.756
r_mcangle_it	5.242
r_mcangle_other	5.24
r_mcbond_it	3.895
r_mcbond_other	3.887
r_angle_refined_deg	1.615
r_angle_other_deg	0.536
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2016
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
MOLREP	phasing
xia2	data reduction