7OZX | pdb_00007ozx

Structure of human galactokinase 1 bound with azepan-1-yl(2,6-difluorophenyl)methanone

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q3X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of:sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate and sodium oxamate).

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.456	α = 90
b = 114.499	β = 100.57
c = 120.822	γ = 90

Symmetry
Space Group	P 1 21 1

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 PILATUS 6M		2018-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	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	2.11	114.5	99.8	0.092	0.109	0.059	0.989	6.2	3.3		112716

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	2.11	2.15	99.8		0.865	1.054	0.595	0.62		3

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	6Q3X	2.3	82.57	82689	4272	99.66	0.2107	0.2083	0.22	0.2577	0.26	RANDOM	48.171

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		-2.14	3.7		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.381
r_dihedral_angle_4_deg	18.537
r_dihedral_angle_3_deg	16.67
r_dihedral_angle_1_deg	7.949
r_angle_refined_deg	1.599
r_angle_other_deg	1.312
r_chiral_restr	0.068
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.381
r_dihedral_angle_4_deg	18.537
r_dihedral_angle_3_deg	16.67
r_dihedral_angle_1_deg	7.949
r_angle_refined_deg	1.599
r_angle_other_deg	1.312
r_chiral_restr	0.068
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11041
Nucleic Acid Atoms
Solvent Atoms	621
Heterogen Atoms	148

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
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 R01GM157729.