1X8K

Crystal structure of retinol dehydratase in complex with anhydroretinol and inactive cofactor PAP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	289	7.5% PEG4000, 0.1M Na Hepes, 0.05M calcium chloride, 4% glycerol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.286	α = 90
b = 66.661	β = 110.66
c = 84.464	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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2000-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.75	100	96.8	0.113	7.8	3.9		20545		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.85	81.5		0.404	1.9	2.3	1612

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	pdb entry 1FMJ	2.75	15	19249	19249	1822	95.51	0.199	0.19905	0.19363	0.25506	RANDOM	16.682

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]
0.44		-1.04	-0.86		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.789
r_scangle_it	2.168
r_angle_refined_deg	1.525
r_scbond_it	1.31
r_mcangle_it	0.809
r_mcbond_it	0.398
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.145

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.789
r_scangle_it	2.168
r_angle_refined_deg	1.525
r_scbond_it	1.31
r_mcangle_it	0.809
r_mcbond_it	0.398
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.103
r_metal_ion_refined	0.051
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5696
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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 R01GM133198.