9SRP | pdb_00009srp

Structure of the Diels-Alderase ChlE3 in complex with cofactor FAD

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	0.2 M Lithium chloride, 0.1 M Tris-HCl, pH 8, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 191.87	α = 90
b = 69.76	β = 109.37
c = 188.72	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 6M		2023-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.99987	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.84	90.669	100	0.996	8.2	6.6		204156

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	1.84	1.87	100		0.322	0.7	6.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.84	90.669	204156	10262	99.947	0.185	0.1831	0.1826	0.2226	0.2221	54.318

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]
-0.717		0.529	1.556		-0.971

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.841
r_dihedral_angle_3_deg	14.256
r_dihedral_angle_2_deg	12.181
r_lrange_other	8.714
r_lrange_it	8.707
r_scangle_it	7.377
r_scangle_other	7.377
r_dihedral_angle_1_deg	7.224
r_scbond_other	5.313
r_scbond_it	5.312
r_mcangle_other	5.04
r_mcangle_it	5.039
r_mcbond_it	3.847
r_mcbond_other	3.847
r_angle_refined_deg	2.348
r_angle_other_deg	0.797
r_symmetry_nbd_refined	0.255
r_dihedral_angle_other_2_deg	0.23
r_nbd_refined	0.222
r_nbd_other	0.198
r_symmetry_nbd_other	0.196
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.115
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.071
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14288
Nucleic Acid Atoms
Solvent Atoms	502
Heterogen Atoms	212

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing