6HSA

The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	20% PEG 4000, 0.2M Ammonium sulfate, 0.1M sodium citrate pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.476	α = 90
b = 79.476	β = 90
c = 72.033	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2016-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.826560	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim I (All)	CC (Half)	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	0.92	31.93	96.7	0.046	0.055	0.03	0.997	14.1	3.2		112975			6.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.923	0.939	85.9		0.331	0.426	0.265	0.762	2.6	2.2

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	6HS9	0.92	31.93	107213	5762	96.73	0.1022	0.1013	0.1198	RANDOM	12.663

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]
-0.08	-0.04		-0.08		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.466
r_sphericity_free	28.099
r_dihedral_angle_4_deg	14.446
r_dihedral_angle_3_deg	12.557
r_sphericity_bonded	9.325
r_dihedral_angle_1_deg	6.137
r_rigid_bond_restr	3.712
r_angle_refined_deg	2.04
r_angle_other_deg	0.729
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.466
r_sphericity_free	28.099
r_dihedral_angle_4_deg	14.446
r_dihedral_angle_3_deg	12.557
r_sphericity_bonded	9.325
r_dihedral_angle_1_deg	6.137
r_rigid_bond_restr	3.712
r_angle_refined_deg	2.04
r_angle_other_deg	0.729
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1150
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	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 R01GM133198.