1YDE

Crystal Structure of Human Retinal Short-Chain Dehydrogenase/Reductase 3

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Magnesium Acetate, MPD, cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	49.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.115	α = 90
b = 98.823	β = 115.87
c = 167.463	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	ADSC QUANTUM 4		2004-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.9794	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.4	30	92	0.117	0.117	9.1	3.2	176307	176307			34.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	0.648		0.706	0.706	1.8	2.4	17963

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.4	30	172629	172629	3559	91.88	0.18166	0.18166	0.18067	0.22903	RANDOM	5.147

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]
1.69		0.75	-2.41		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.459
r_dihedral_angle_4_deg	20.4
r_dihedral_angle_3_deg	16.884
r_scangle_it	5.927
r_dihedral_angle_1_deg	5.808
r_scbond_it	4.158
r_mcangle_it	2.116
r_angle_refined_deg	1.505
r_mcbond_it	1.413
r_angle_other_deg	0.919
r_mcbond_other	0.346
r_symmetry_vdw_other	0.274
r_symmetry_hbond_refined	0.227
r_nbd_refined	0.206
r_nbd_other	0.186
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.171
r_symmetry_vdw_refined	0.154
r_chiral_restr	0.088
r_nbtor_other	0.088
r_xyhbond_nbd_other	0.073
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	29359
Nucleic Acid Atoms
Solvent Atoms	1251
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing