Experiment: 1JXK

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	298	MPD, calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP at 298K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.9	α = 90
b = 75.737	β = 90
c = 134.554	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	200	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2000-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	67.42	98.31	0.057	0.057	21.9	3.5	39061	38401	2	2	16.857

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.949	99		0.057	0.155	8.6

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1SMD	1.9	67.42	39061	38401	4300	98.31	0.1761	0.17615	0.17346	0.19997	RANDOM	16.857

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.794
r_dihedral_angle_1_deg	4.249
r_scangle_it	2.589
r_scbond_it	1.635
r_angle_refined_deg	1.32
r_mcangle_it	1.121
r_mcbond_it	0.594
r_xyhbond_nbd_refined	0.215
r_xyhbond_nbd_other	0.123
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.794
r_dihedral_angle_1_deg	4.249
r_scangle_it	2.589
r_scbond_it	1.635
r_angle_refined_deg	1.32
r_mcangle_it	1.121
r_mcbond_it	0.594
r_xyhbond_nbd_refined	0.215
r_xyhbond_nbd_other	0.123
r_chiral_restr	0.096
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_nbtor_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3923
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

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.