5E26 | pdb_00005e26

Crystal structure of human PANK2: the catalytic core domain in complex with pantothenate and adenosine diphosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SMS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	2.4M Na Malonate pH 6.5, 0.1M TCEP HCl

Crystal Properties
Matthews coefficient	Solvent content
2.62	52.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.874	α = 90
b = 109.717	β = 90
c = 142.571	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	CCD	ADSC QUANTUM 315r		2015-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.14	50	100	0.15	0.157	0.057	5.1	8.1		96028

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.14	2.18	100		0.94	0.351	0.791		8.1	4721

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	3SMS	2.14	50.01	93190	1462	99.98	0.2146	0.214	0.22	0.2505	0.25	RANDOM	34.084

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]
0.66			0.75		-1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.273
r_dihedral_angle_4_deg	16.993
r_dihedral_angle_3_deg	13.019
r_dihedral_angle_1_deg	5.825
r_mcangle_it	2.122
r_mcbond_it	1.34
r_mcbond_other	1.34
r_angle_refined_deg	1.282
r_angle_other_deg	0.897
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.273
r_dihedral_angle_4_deg	16.993
r_dihedral_angle_3_deg	13.019
r_dihedral_angle_1_deg	5.825
r_mcangle_it	2.122
r_mcbond_it	1.34
r_mcbond_other	1.34
r_angle_refined_deg	1.282
r_angle_other_deg	0.897
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11071
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	191

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction

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.