1X8L | pdb_00001x8l

Crystal structure of retinol dehydratase in complex with all-trans-4-oxoretinol and inactive cofactor PAP

X-RAY DIFFRACTION

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Starting Model(s)

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

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
2.64	53.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.506	α = 90
b = 67.192	β = 111.85
c = 85.066	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	2000-10-17	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	2.1	100	89	0.093	13.3	2.7		45373		-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)
	2.1	2.15	96		0.408	2.4	2.5	3230

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1FMJ	2.1	15	40422	40422	3121	88.4	0.19853	0.19853	0.19564	0.23134	RANDOM	22.609

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]
-0.52		-0.59	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.49
r_scangle_it	2.905
r_scbond_it	1.837
r_angle_refined_deg	1.588
r_mcangle_it	1.238
r_angle_other_deg	0.886
r_mcbond_it	0.701
r_symmetry_vdw_other	0.262
r_symmetry_vdw_refined	0.242
r_nbd_other	0.233
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.181
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.094
r_nbtor_other	0.085
r_metal_ion_refined	0.051
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5685
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing