4JAX | pdb_00004jax

Crystal structure of dimeric KlHxk1 in crystal form X

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O1W	chain A of PDB entry 3O1W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	1 microliter protein (7.8 mg/ml KlHxk1 in buffer (10 mM Tris, 1 mM EDTA, 1 mM DTT, 0.5 mM PMSF, pH 7.4)) + 1 microliter reservoir (2.2 M (NH4)2HPO4, 0.1 M Tris pH 8.5), micro seeding, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.81	α = 90
b = 178.3	β = 90
c = 216.21	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	MARMOSAIC 225 mm CCD	mirror	2008-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.26	29.85	99.8	0.049	24.25	5.2	191251	190903		-3	47.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.26	2.32	100		0.502	3.84	5.2	14012

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	chain A of PDB entry 3O1W	2.26	29.602	191035	190815	1912	99.83	0.2007	0.2003	0.2	0.2398	0.24	RANDOM	49.6244

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]
0.57			-0.25		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.155
r_dihedral_angle_4_deg	20.853
r_dihedral_angle_3_deg	15.97
r_dihedral_angle_1_deg	5.828
r_angle_refined_deg	1.502
r_chiral_restr	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_mcbond_it
r_mcbond_other

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.155
r_dihedral_angle_4_deg	20.853
r_dihedral_angle_3_deg	15.97
r_dihedral_angle_1_deg	5.828
r_angle_refined_deg	1.502
r_chiral_restr	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21972
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	133

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	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.