7NB2 | pdb_00007nb2

Crystal structure of human choline alpha in complex with an inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CKQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	18-20% Peg-mme 5000, 0.1 M Magnesium Formate, 0.1 M HEPES pH 7.0.

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.593	α = 90
b = 120.926	β = 90
c = 130.456	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 XE 16M		2020-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.4	55.59	99.7	0.063	19	9.9		35130

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	99.9		0.689		9.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	2CKQ	2.4	51.196	35071	1718	99.571	0.204	0.2017	0.2	0.2477	0.25	62.682

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]
-1.157			5.936		-4.779

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.525
r_dihedral_angle_4_deg	17.865
r_dihedral_angle_3_deg	17.302
r_lrange_it	10.784
r_scangle_it	8.583
r_mcangle_it	7.13
r_dihedral_angle_1_deg	6.395
r_scbond_it	6.228
r_mcbond_it	4.895
r_angle_refined_deg	1.389

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.525
r_dihedral_angle_4_deg	17.865
r_dihedral_angle_3_deg	17.302
r_lrange_it	10.784
r_scangle_it	8.583
r_mcangle_it	7.13
r_dihedral_angle_1_deg	6.395
r_scbond_it	6.228
r_mcbond_it	4.895
r_angle_refined_deg	1.389
r_nbtor_refined	0.316
r_nbd_refined	0.223
r_symmetry_xyhbond_nbd_refined	0.176
r_symmetry_nbd_refined	0.166
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.106
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5702
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	99

Software

Software
Software Name	Purpose
REFMAC	refinement
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 R01GM157729.