6Q91 | pdb_00006q91

Structure of human galactokinase 1 bound with 5-Chloro-N-isobutyl-2-methoxybenzamide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M MOPS/sodium HEPES, 40-50% Morpheus precipitant mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1M morpheus carboxylic acids mix (0.02M each of sodium formate, ammonium actetate, sodium citrate tribasic dihydrate, sodium oxamate, potassium sodium tartrate tetrahydrate

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.323	α = 90
b = 114.959	β = 100.79
c = 120.918	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	2.27	82.74	99.6	0.111	0.131	0.07	0.996	4.7	3.4		91197

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	2.27	2.39	99.9		1.393	1.648	0.873	0.616		3.5

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	1wuu	2.4	82.74	72868	3787	99.46	0.2193	0.2159	0.22	0.2855	0.29	RANDOM	44.518

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]
0.22		-2.59	4.41		-3.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.866
r_dihedral_angle_4_deg	18.139
r_dihedral_angle_3_deg	16.469
r_dihedral_angle_1_deg	8.2
r_angle_refined_deg	1.772
r_angle_other_deg	1.322
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.866
r_dihedral_angle_4_deg	18.139
r_dihedral_angle_3_deg	16.469
r_dihedral_angle_1_deg	8.2
r_angle_refined_deg	1.772
r_angle_other_deg	1.322
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11006
Nucleic Acid Atoms
Solvent Atoms	325
Heterogen Atoms	178

Software

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