6SMT | pdb_00006smt

S-enantioselective imine reductase from Mycobacterium smegmatis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G6R	5G6R, 3ZGY, 4OQY, 4D3S
experimental model	PDB	3ZGY	5G6R, 3ZGY, 4OQY, 4D3S
experimental model	PDB	4OQY	5G6R, 3ZGY, 4OQY, 4D3S
experimental model	PDB	4D3S	5G6R, 3ZGY, 4OQY, 4D3S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	20 % (w/v) PEG 3350, 0.2 M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.007	α = 90
b = 77.023	β = 90.2
c = 194.485	γ = 90

Symmetry
Space Group	I 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 PILATUS 6M-F		2018-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9762	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.55	100.42	99.1	0.073	0.08	0.03	0.997	13.2	6.9		248023

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	1.55	1.58	96.3		0.384	0.417	0.162	0.928		6.4

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 (Observed)	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	5G6R, 3ZGY, 4OQY, 4D3S	1.55	100.42	235772	12250	99.13	0.132	0.1308	0.131	0.1549	0.1551	RANDOM	18.425

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]
0.22		0.03	-0.36		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.737
r_dihedral_angle_4_deg	15.286
r_dihedral_angle_3_deg	12.795
r_dihedral_angle_1_deg	5.869
r_angle_refined_deg	2.267
r_angle_other_deg	1.739
r_chiral_restr	0.127
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10376
Nucleic Acid Atoms
Solvent Atoms	1970
Heterogen Atoms	364

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction