3KO6 | pdb_00003ko6

Crystal structure of yeast free methionine-R-sulfoxide reductase Ykg9 in complex with the substrate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	0.1M Tris pH 8.0, 2.0M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.548	α = 90
b = 73.548	β = 90
c = 163.56	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	MAR scanner 345 mm plate		2009-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.55	50	99.2	0.123	0.092	15.1	6	15410	15274

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)
	2.55	2.64	95.3		0.499	0.412	2.2	3.6	1421

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.55	49.561	14488	761	99.35	0.21045	0.20825	0.2	0.25408	0.25	RANDOM	32.016

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]
-0.2			-0.2		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.259
r_dihedral_angle_3_deg	14.921
r_dihedral_angle_1_deg	5.671
r_scangle_it	2.651
r_scbond_it	1.547
r_mcangle_it	1.289
r_angle_refined_deg	1.178
r_mcbond_it	0.697
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2718
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	20

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling