7R5T | pdb_00007r5t

CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT F254I COMPLEXED WITH FE, NADH, AND GLYCEROL

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	0.2M Magnesium chloride hexahydrate; 0.1M Bis-Tris, pH 5.5; 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.559	α = 90
b = 54.329	β = 99.97
c = 101.795	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 PILATUS3 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	1.85	61.841	99.9	0.056	0.993	7.3	3.2		64213			19.5

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	1.85	1.89	100		0.273	0.85	1.9	3.3

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	1.85	61.841	64190	3176	99.852	0.184	0.1824	0.19	0.2154	0.22	26.386

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]
-2.815		-0.794	3.146		-0.049

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.758
r_dihedral_angle_4_deg	14.28
r_dihedral_angle_3_deg	12.215
r_dihedral_angle_1_deg	6.436
r_lrange_it	4.015
r_lrange_other	3.993
r_scangle_it	2.855
r_scangle_other	2.854
r_mcangle_it	2.03
r_mcangle_other	2.03
r_scbond_it	1.771
r_scbond_other	1.771
r_mcbond_it	1.33
r_mcbond_other	1.33
r_angle_refined_deg	1.3
r_angle_other_deg	1.254
r_nbd_refined	0.196
r_symmetry_nbd_other	0.166
r_nbd_other	0.157
r_nbtor_refined	0.148
r_symmetry_nbd_refined	0.148
r_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_refined	0.075
r_chiral_restr	0.061
r_bond_refined_d	0.005
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	5692
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	210

Software

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