Experiment: 1JDB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		0.65M TETRAETHYL AMMONIUM CHLORIDE (E4NCL) 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 25MM HEPES PH 7.4. THE CRYSTAL WAS SOAKED INTO: 1.4M E4NCL 8% PEG 8000 250MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 25MM GLUTAMINE 25MM HEPES PH 7.4 7.5% ETHYLENE GLYCOL.

Crystal Properties
Matthews coefficient	Solvent content
3	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.8	α = 90
b = 167.7	β = 90
c = 323	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	120	IMAGE PLATE	MARRESEARCH		1997-07-22	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1

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	2.1	30	90	0.059	0.059	22.9	4.1		404724

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	2.1	2.18	73		0.203	0.203	3.2	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1JDB	2.1	30	404724	404724		90	0.179

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
t_it	500
t_dihedral_angle_d	17.6
t_angle_deg	2.61
t_nbd	0.034
t_bond_d	0.011
t_gen_planes	0.009
t_trig_c_planes	0.004
t_incorr_chiral_ct
t_pseud_angle

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	44220
Nucleic Acid Atoms
Solvent Atoms	4857
Heterogen Atoms	487

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
TNT	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.