7R3D | pdb_00007r3d

CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N151G, L259V COMPLEXED WITH FE, NADH, AND GLYCEROL (Absence of Nicotinamide ring)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RRM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295.15	0.1M Bistris pH 5.5; 25% Polyethylene glycol 8000; 0.2M ammonium formate 9.25 mg/ml dissolved in 20mM Tris-HCl, pH7.5 that was supplemented with 0.5mM Fe and 10mM NADH and incubated for 10 min at room temperature.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.96	α = 90
b = 95.11	β = 116.48
c = 69.36	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 PILATUS 6M		2021-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9999	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	48.53	99	0.038	0.997	10.9	3.12		141933			16.97

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	99		0.405	0.807	2.2	2.86

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1RRM	1.4	48.53	141898	6883	98.934	0.158	0.1564	0.17	0.1794	0.19	18.664

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]
0.914		0.095	0.886		-1.266

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.454
r_dihedral_angle_4_deg	16.163
r_dihedral_angle_3_deg	11.749
r_dihedral_angle_1_deg	6.33
r_lrange_it	3.687
r_lrange_other	3.542
r_scangle_it	2.62
r_scangle_other	2.619
r_scbond_it	1.697
r_scbond_other	1.696
r_mcangle_it	1.553
r_mcangle_other	1.552
r_angle_other_deg	1.459
r_angle_refined_deg	1.398
r_mcbond_it	1.029
r_mcbond_other	1.028
r_nbd_refined	0.216
r_symmetry_nbd_refined	0.17
r_symmetry_nbd_other	0.165
r_nbtor_refined	0.162
r_nbd_other	0.152
r_xyhbond_nbd_refined	0.12
r_symmetry_xyhbond_nbd_refined	0.116
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5700
Nucleic Acid Atoms
Solvent Atoms	595
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing