2PD6

Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q7B	Swissmodel based on pdb entries 1Q7B and 1EDO
experimental model	PDB	1EDO	Swissmodel based on pdb entries 1Q7B and 1EDO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	200 mM sodium fluoride, 20% PEG3350, 10% ethylene glycol plus 5mM NAD+, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.839	α = 90
b = 62.429	β = 99.22
c = 102.439	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	MARMOSAIC 225 mm CCD		2007-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00234	SLS	X10SA

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	99.9	0.117		3.5		54998

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)
1	2	2.07	100		0.759		3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Swissmodel based on pdb entries 1Q7B and 1EDO	2	46	54998	54998	2937	99.6	0.18616	0.18616	0.18394	0.22667	RANDOM	31.061

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]
-1.1		-0.05	0.86		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.96
r_dihedral_angle_4_deg	14.421
r_dihedral_angle_3_deg	12.584
r_dihedral_angle_1_deg	5.641
r_scangle_it	3.062
r_scbond_it	2.025
r_angle_refined_deg	1.354
r_mcangle_it	1.228
r_angle_other_deg	0.896
r_mcbond_it	0.802
r_symmetry_hbond_refined	0.433
r_symmetry_vdw_other	0.273
r_symmetry_vdw_refined	0.205
r_nbd_refined	0.203
r_mcbond_other	0.194
r_nbd_other	0.183
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.129
r_nbtor_other	0.087
r_chiral_restr	0.075
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6605
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	176

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing