5C7H

Crystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021 in complex with NADPH

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG 2 condition #28 (0.2 M Ammonium Citrate Tribasic pH 7.0, 20% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 1 mg/ml TEV solution at 289 K for 1 hour

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.049	α = 90
b = 78.669	β = 90
c = 79.537	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	CCD	MARMOSAIC 300 mm CCD	Beryllium Lenses	2015-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.3	50	99.9	0.052	0.02	0.057	0.023	9.2	5.9	68811	68759		-3	12.1

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	1.3	1.32	100		0.67	0.744	0.318	0.749	2.1	5.4	3380

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4XAP	1.3	50	65197	3483	99.9	0.1165	0.1152	0.1401	RANDOM	15.157

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]
0.06			-0.16		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.524
r_sphericity_free	24.475
r_dihedral_angle_4_deg	16.474
r_sphericity_bonded	11.664
r_dihedral_angle_3_deg	11.076
r_dihedral_angle_1_deg	5.461
r_angle_other_deg	1.966
r_mcangle_it	1.705
r_angle_refined_deg	1.46
r_mcbond_it	1.332

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.524
r_sphericity_free	24.475
r_dihedral_angle_4_deg	16.474
r_sphericity_bonded	11.664
r_dihedral_angle_3_deg	11.076
r_dihedral_angle_1_deg	5.461
r_angle_other_deg	1.966
r_mcangle_it	1.705
r_angle_refined_deg	1.46
r_mcbond_it	1.332
r_mcbond_other	1.332
r_rigid_bond_restr	1.249
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2107
Nucleic Acid Atoms
Solvent Atoms	432
Heterogen Atoms	48

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
REFMAC	refinement
HKL-3000	phasing
MLPHARE	phasing
SHELX	phasing
HKL-3000	data scaling
HKL-3000	data reduction
BLU-MAX	data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.