2ABB

Structure of PETN reductase Y186F in complex with cyanide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VYR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	293	25%(w/v) PEG 3000, 0.1M trisodium citrate, 0.1M cacodylic acid(pH 6.2), 17%(v/v) isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	43.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.618	α = 90
b = 68.664	β = 90
c = 88.602	γ = 90

Symmetry
Space Group	P 21 21 21

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		2003-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9	ESRF	ID14-1

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	1	15	98.2	0.087	11.1	4.2	172733	169624

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	1	1.03	84		0.489	1.9	3.1

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	1VYR	1	14.37	172733	169624	8938	98.2	0.13924	0.13924	0.1384	0.15486	RANDOM	10.713

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]
-0.57			0.82		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.705
r_dihedral_angle_4_deg	14.115
r_dihedral_angle_3_deg	11.898
r_dihedral_angle_1_deg	5.809
r_sphericity_free	4.392
r_sphericity_bonded	2.878
r_scangle_it	2.752
r_scbond_it	1.882
r_angle_refined_deg	1.513
r_mcangle_it	1.501
r_angle_other_deg	1.2
r_mcbond_it	1.004
r_rigid_bond_restr	0.934
r_mcbond_other	0.496
r_symmetry_vdw_refined	0.476
r_symmetry_vdw_other	0.343
r_nbd_other	0.259
r_nbd_refined	0.254
r_symmetry_hbond_refined	0.237
r_xyhbond_nbd_refined	0.136
r_nbtor_other	0.087
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbtor_refined
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2716
Nucleic Acid Atoms
Solvent Atoms	656
Heterogen Atoms	38

Software

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