9SI5 | pdb_00009si5

Crystal structure of DoxA in complex with reaction intermediate DHD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9S7F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	0.1M MES pH6.0; 0.2M NH4Cl; 20% (w/v) PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.873	α = 90
b = 108.058	β = 90
c = 179.772	γ = 90

Symmetry
Space Group	C 2 2 21

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 S 9M		2024-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	1	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.54	89.89	99.4	0.304	0.359	0.188	0.874	2.9	6.6		32896

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.54	2.65			2.09	2.563	1.45	0.472		5.3

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	2.54	89.89	32714	1640	98.858	0.236	0.2335	0.2318	0.281	0.2761	69.427

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]
-0.361			2.496		-2.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.739
r_dihedral_angle_6_deg	15.65
r_dihedral_angle_2_deg	15.312
r_lrange_it	9.104
r_lrange_other	9.088
r_dihedral_angle_1_deg	7.311
r_scangle_it	5.224
r_scangle_other	5.224
r_mcangle_it	4.882
r_mcangle_other	4.881
r_scbond_it	3.183
r_scbond_other	3.182
r_mcbond_it	2.935
r_mcbond_other	2.935
r_angle_refined_deg	2.331
r_dihedral_angle_other_2_deg	2.11
r_angle_other_deg	0.778
r_symmetry_nbd_refined	0.36
r_nbd_other	0.317
r_symmetry_xyhbond_nbd_other	0.269
r_symmetry_xyhbond_nbd_refined	0.269
r_nbd_refined	0.262
r_xyhbond_nbd_refined	0.245
r_symmetry_nbd_other	0.227
r_nbtor_refined	0.199
r_symmetry_nbtor_other	0.094
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6287
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	162

Software

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