3LS6

Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase in complex with sulfate and zinc

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G57

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	30% PEG 5000 MME, 100mM MES Sodium Salt, 200mM Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.276	α = 90
b = 77.161	β = 90
c = 146.827	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	MAR scanner 345 mm plate	OSMIC VARIMAX	2009-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.542

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	1.86	73.41	99.3	0.052	0.052	29.2	5.2	31811	31811			20.34

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)
1	1.86	1.92	99.7		0.192	0.185	9.32	4.8	3140

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	1G57	1.86	50	31811	31803	1614	99.26	0.16104	0.16104	0.15919	0.19662	RANDOM	20.347

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]
0.4			-0.57		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.427
r_dihedral_angle_4_deg	15.378
r_dihedral_angle_3_deg	13.536
r_dihedral_angle_1_deg	5.369
r_scangle_it	4.037
r_scbond_it	2.294
r_angle_refined_deg	1.322
r_mcangle_it	1.298
r_mcbond_it	0.696
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.427
r_dihedral_angle_4_deg	15.378
r_dihedral_angle_3_deg	13.536
r_dihedral_angle_1_deg	5.369
r_scangle_it	4.037
r_scbond_it	2.294
r_angle_refined_deg	1.322
r_mcangle_it	1.298
r_mcbond_it	0.696
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3041
Nucleic Acid Atoms
Solvent Atoms	335
Heterogen Atoms	33

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.