6HS9 | pdb_00006hs9

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

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	10% PEG 8000, 0.1M CaCl2, 0.1M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.55	α = 90
b = 79.55	β = 90
c = 72.28	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)	Rrim I (All)	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	1.05	32.04	99.5	0.054	0.047	0.028	0.998	13.9	4.8		119959			12.298

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	1.05	1.07	98.8		0.717	0.914	0.559	0.477	1.4	2.4

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	1GQO	1.05	32	74983	4062	99.26	0.1139	0.1128	0.12	0.134	0.14	RANDOM	21.112

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]
-0.21	-0.1		-0.21		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.998
r_dihedral_angle_4_deg	26.117
r_sphericity_free	24.668
r_dihedral_angle_3_deg	13.488
r_sphericity_bonded	12.956
r_dihedral_angle_1_deg	5.862
r_rigid_bond_restr	5.076
r_angle_refined_deg	2.051
r_angle_other_deg	0.712
r_chiral_restr	0.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.998
r_dihedral_angle_4_deg	26.117
r_sphericity_free	24.668
r_dihedral_angle_3_deg	13.488
r_sphericity_bonded	12.956
r_dihedral_angle_1_deg	5.862
r_rigid_bond_restr	5.076
r_angle_refined_deg	2.051
r_angle_other_deg	0.712
r_chiral_restr	0.129
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1150
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms	19

Software

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

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.