6EFH

Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyruvamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VK4	PDB entry 2VK4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.25	281.15	2 mg/mL KlPDC in 2 mM MES, 18 mM citrate, pH 6.25, 4 mM thiamine diphosphate, 4 mM magnesium sulfate, 2 mM DTT, 1:1 with mother liquor (18-24% w/v PEG2000/PEG6000), ~25 days at 8 degrees C, soaked for 50 seconds in 2 uL mother liquor + 2 uL 90% v/v PEG400, 200 mM pyruvamide prior to flash freezing

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 172.765	α = 90
b = 172.765	β = 90
c = 210.083	γ = 90

Symmetry
Space Group	I 4 2 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	CCD	ADSC QUANTUM 4		2007-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.93300	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	2.99	55.6	100	0.333	9	14.4		32279			25.68

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	2.99	3.05	100		1.797	1.6	14.7

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 2VK4	2.99	55.6	31223	1055	100	0.181	0.178	0.265	RANDOM	42.52

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]
1.94			1.94		-3.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.609
r_dihedral_angle_4_deg	20.327
r_dihedral_angle_3_deg	19.268
r_dihedral_angle_1_deg	8.406
r_long_range_B_refined	7.526
r_long_range_B_other	7.526
r_mcangle_it	5.17
r_mcangle_other	5.169
r_scangle_other	4.882
r_mcbond_it	3.213
r_mcbond_other	3.2
r_scbond_it	2.985
r_scbond_other	2.985
r_angle_refined_deg	1.465
r_angle_other_deg	0.859
r_chiral_restr	0.064
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8587
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing