5DAN

Crystal structure of a novel aldo keto reductase Tm1743 from Thermotoga maritima in complex with NADP+

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	289	0.2 M Calcium chloride dehydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 20 % v/v 2-Propanol

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.821	α = 90
b = 84.821	β = 90
c = 93.727	γ = 120

Symmetry
Space Group	P 31 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	IMAGE PLATE	RIGAKU RAXIS IV++		2014-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	50	95.8	0.1	9.8	10		25576

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	98.4		3.3	9.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1PYF	2	42.41	24240	1285	95.7	0.2063	0.2047	0.2369	RANDOM	35.755

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]
0.7	0.35		0.7		-2.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.251
r_dihedral_angle_4_deg	18.77
r_dihedral_angle_3_deg	16.14
r_dihedral_angle_1_deg	5.937
r_mcangle_it	2.652
r_mcbond_it	1.924
r_mcbond_other	1.923
r_angle_refined_deg	1.639
r_angle_other_deg	1.027
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.251
r_dihedral_angle_4_deg	18.77
r_dihedral_angle_3_deg	16.14
r_dihedral_angle_1_deg	5.937
r_mcangle_it	2.652
r_mcbond_it	1.924
r_mcbond_other	1.923
r_angle_refined_deg	1.639
r_angle_other_deg	1.027
r_chiral_restr	0.093
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2206
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.