2DM6

Crystal structure of anti-configuration of indomethacin and leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complex

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	oil batch	6.4	298	20% PEG 4000, 50mM magnesium chloride, 0.1M MES, pH 6.4, oil batch, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.253	α = 90
b = 76.075	β = 102.62
c = 79.646	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	CCD	RIGAKU JUPITER		2004-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00000	SPring-8	BL45XU

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	97.9	0.07	51.9			45006

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	84.1	84.1	0.179

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2	34.16	45006	44983	2216	97.9	0.183	0.181	0.224	RANDOM	26.06

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]
		0.04	-0.01		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.075
r_dihedral_angle_4_deg	16.634
r_dihedral_angle_3_deg	12.861
r_scangle_it	6.225
r_dihedral_angle_1_deg	5.213
r_scbond_it	4.352
r_mcangle_it	2.747
r_mcbond_it	2.086
r_angle_refined_deg	1.115
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.075
r_dihedral_angle_4_deg	16.634
r_dihedral_angle_3_deg	12.861
r_scangle_it	6.225
r_dihedral_angle_1_deg	5.213
r_scbond_it	4.352
r_mcangle_it	2.747
r_mcbond_it	2.086
r_angle_refined_deg	1.115
r_nbtor_refined	0.297
r_nbd_refined	0.184
r_symmetry_vdw_refined	0.157
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5079
Nucleic Acid Atoms
Solvent Atoms	600
Heterogen Atoms	132

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
CNS	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.