2VK8

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with its substrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VK1	PDB ENTRY 2VK1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.35	273.15	15MM CITRATE, 1.67MM MES, 315MM PYRUVATE, 1MM NADH, 0.001MG/ML ALCOHOL DEHYDROGENASE, 1.67MM TDP, 1.67MM MAGNESIUM SULFATE, 1.67MM DTT, 11.25% PEG2000, 11.25% PEG 6000, 1.1MG SCPDC/ML, PH 6.35, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273.15K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.98	α = 90
b = 190.51	β = 113.01
c = 84.14	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 CCD		2007-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.42	99	99.7	0.05	22.5	4.4		427276		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.44	99.8		0.63	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2VK1	1.42	95.35	425935	1068	99.6	0.181	0.181	0.186	RANDOM	18.93

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]
0.17		-0.19	-0.06		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.998
r_dihedral_angle_4_deg	16.612
r_dihedral_angle_3_deg	12.571
r_dihedral_angle_1_deg	5.39
r_scangle_it	2.592
r_scbond_it	1.67
r_angle_refined_deg	1.25
r_mcangle_it	1.027
r_mcbond_it	0.557
r_chiral_restr	0.53
r_nbtor_refined	0.31
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.182
r_symmetry_vdw_refined	0.148
r_xyhbond_nbd_refined	0.101
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17292
Nucleic Acid Atoms
Solvent Atoms	1818
Heterogen Atoms	132

Software

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