Experiment: 1JXJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SMD	PDB Entry 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, temperature 298K, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.295	α = 90
b = 75.25	β = 90
c = 135.018	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	2001-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	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	1.99	65.94	97.7	0.062	0.051	16.2	3.2	36288	34452		2	23

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)
	1.99	2.07	95		0.062	0.281	3

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	PDB Entry 1SMD	1.99	65.94	34452	34452	1795	97.7	0.1661	0.16615	0.16448	0.19835	RANDOM	22.987

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_1_deg	4.826
r_scangle_it	3.419
r_scbond_it	2.299
r_angle_refined_deg	1.617
r_mcangle_it	1.412
r_mcbond_it	0.798
r_xyhbond_nbd_refined	0.22
r_chiral_restr	0.129
r_dihedral_angle_3_deg	0.129
r_xyhbond_nbd_other	0.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.826
r_scangle_it	3.419
r_scbond_it	2.299
r_angle_refined_deg	1.617
r_mcangle_it	1.412
r_mcbond_it	0.798
r_xyhbond_nbd_refined	0.22
r_chiral_restr	0.129
r_dihedral_angle_3_deg	0.129
r_xyhbond_nbd_other	0.123
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_nbtor_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3940
Nucleic Acid Atoms
Solvent Atoms	294
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.