9TOX | pdb_00009tox

CO dehydrogenase 2 variant A559W

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B51

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291.15	PEG 2000MME

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.31	α = 90
b = 75.33	β = 111.56
c = 71.59	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 S 6M		2025-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	1.49	40.77	99.4	0.998	9.81	3.41		175782

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	1.49	1.58			0.322

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.49	40.799	89567	1071	99.88	0.175	0.1749	0.1755	0.2126	0.2132	RANDOM	13.54

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]
0.576		-0.486	-1.246		0.803

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.631
r_dihedral_angle_3_deg	13.953
r_scangle_other	10.101
r_scangle_it	10.083
r_dihedral_angle_1_deg	9.322
r_lrange_other	9.212
r_lrange_it	9.194
r_scbond_other	9.012
r_scbond_it	8.97
r_mcangle_other	4.951
r_mcangle_it	4.95
r_mcbond_it	4.306
r_mcbond_other	4.303
r_angle_refined_deg	2.048
r_angle_other_deg	0.482
r_chiral_restr	0.37
r_nbd_refined	0.223
r_symmetry_nbd_other	0.19
r_nbd_other	0.173
r_nbtor_refined	0.165
r_symmetry_nbd_refined	0.158
r_symmetry_metal_ion_refined	0.157
r_metal_ion_refined	0.151
r_xyhbond_nbd_refined	0.125
r_symmetry_xyhbond_nbd_refined	0.082
r_symmetry_nbtor_other	0.074
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4663
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
XSCALE	data scaling