8A5Z | pdb_00008a5z

Imine Reductase from Ensifer adhaerens A208N mutant in complex with NADP+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8A3X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	279	20 % mPEG 3350 w/v, 3% propan-1-ol v/v, 0.1 M NaI and 0.1 M bis tris propane

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81	α = 90
b = 89	β = 90
c = 94	γ = 90

Symmetry
Space Group	P 21 21 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 XE 16M		2022-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.31	64.63	100	0.18	0.05	1	10.2	13.4		30238			31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.31	2.39	100		1.04	0.3	0.93	1.3	12.6

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	8A3X	2.31	64.63	28908	1540	99.99	0.1998	0.1975	0.2034	0.2423	0.2443	RANDOM	41.676

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]
-5.62			-0.99		6.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.241
r_dihedral_angle_4_deg	17.364
r_dihedral_angle_3_deg	15.781
r_dihedral_angle_1_deg	6.343
r_angle_refined_deg	1.716
r_angle_other_deg	1.362
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4287
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
SCALA	data scaling
REFMAC	phasing