Experiment: 1KJ3

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1.5M K2HPO4/N2HPO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.24	α = 90
b = 90.63	β = 111.51
c = 89.58	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARRESEARCH		1999-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

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	2.3	22.53	99.5	0.046	11.4	3.3	43653	43653

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)
	2.3	2.42	98.9		0.161	4.2	2.5	6306

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	1VAC	2.3	12	42902	42902	4278		0.211	0.211	0.207	0.259	RANDOM	40.57

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]
-4.9		0.3	12.1		-6.7

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	24.2
p_staggered_tor	17.9
p_scangle_it	3.17
p_planar_tor	2.2
p_scbond_it	2.03
p_mcangle_it	2.02
p_mcbond_it	1.11
p_chiral_restr	0.14
p_planar_d	0.027
p_angle_d	0.022

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	24.2
p_staggered_tor	17.9
p_scangle_it	3.17
p_planar_tor	2.2
p_scbond_it	2.03
p_mcangle_it	2.02
p_mcbond_it	1.11
p_chiral_restr	0.14
p_planar_d	0.027
p_angle_d	0.022
p_plane_restr	0.011
p_bond_d	0.009
p_hb_or_metal_coord
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6318
Nucleic Acid Atoms
Solvent Atoms	376
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

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.