6HSQ | pdb_00006hsq

The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37 crystal form 1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RC9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	1M Lithium Sulphate, 0.1M MOPS pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.386	α = 90
b = 139.386	β = 90
c = 139.386	γ = 90

Symmetry
Space Group	P 21 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 6M		2018-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.915870	Diamond	I04-1

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	1.456	98.561	95.9	0.084	0.12	0.028	0.999	14.6	9.9		150335			22.5

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	1.456	1.496	62.6		1.546	1.636	0.532	0.536		9.4

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	4RC9	1.46	98.56	142816	7523	95.89	0.169	0.1682	0.17	0.1858	0.19	RANDOM	25.658

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.131
r_dihedral_angle_4_deg	16.392
r_dihedral_angle_3_deg	12.775
r_dihedral_angle_1_deg	6.583
r_angle_refined_deg	2.151
r_angle_other_deg	1.625
r_chiral_restr	0.125
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.131
r_dihedral_angle_4_deg	16.392
r_dihedral_angle_3_deg	12.775
r_dihedral_angle_1_deg	6.583
r_angle_refined_deg	2.151
r_angle_other_deg	1.625
r_chiral_restr	0.125
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4656
Nucleic Acid Atoms
Solvent Atoms	577
Heterogen Atoms	64

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
AMoRE	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.