2FVL

Crystal structure of human 3-alpha hydroxysteroid/dihydrodiol dehydrogenase (AKR1C4) complexed with NADP+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XF0	1XF0.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	Potassium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
5.999597	79.498619

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.008	α = 90
b = 166.008	β = 90
c = 194.942	γ = 90

Symmetry
Space Group	P 43 21 2

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 HTC		2005-12-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.54180

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	196.12	98.5				104763

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	2.4	2.53	90

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	1XF0.pdb	2.4	32.73	102788	102788	1972	98.35	0.1672	0.1672	0.16648	0.20454	RANDOM	26.205

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]
-0.5			-0.5		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.402
r_dihedral_angle_3_deg	14.402
r_dihedral_angle_4_deg	14.307
r_scangle_it	8.761
r_scbond_it	7.698
r_dihedral_angle_1_deg	6.167
r_mcangle_it	4.683
r_mcbond_it	4.372
r_mcbond_other	1.424
r_angle_refined_deg	1.421
r_angle_other_deg	0.961
r_symmetry_hbond_refined	0.219
r_symmetry_vdw_other	0.214
r_nbd_refined	0.19
r_nbd_other	0.188
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.153
r_symmetry_vdw_refined	0.125
r_chiral_restr	0.086
r_nbtor_other	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7799
Nucleic Acid Atoms
Solvent Atoms	834
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing