2VK1 | pdb_00002vk1

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant D28A 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	1QPB	PDB ENTRY 1QPB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.35	273	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% PEG 2000, 11.25% PEG 6000, 1.1MG SCPDC/ML PH 6.35, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273.15C

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.88	α = 90
b = 141.31	β = 107.19
c = 114.41	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		2007-07-07	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	1.71	99	99.3	0.07	17.5	3.6		262151		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	1.71	1.74	99.2		0.57	2.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QPB	1.71	109.11	260330	1313	99.1	0.191	0.191	0.1902	0.22	0.2191	RANDOM	20.91

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]
-0.09		-0.32	0.78		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.855
r_dihedral_angle_4_deg	19.513
r_dihedral_angle_3_deg	14.173
r_dihedral_angle_1_deg	5.714
r_scangle_it	3.295
r_scbond_it	2.193
r_angle_refined_deg	1.45
r_mcangle_it	1.307
r_mcbond_it	0.755
r_chiral_restr	0.514
r_nbtor_refined	0.309
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.125
r_symmetry_hbond_refined	0.123
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
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	17280
Nucleic Acid Atoms
Solvent Atoms	1558
Heterogen Atoms	156

Software

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