Experiment: 4JNG

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IDX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	298	0.1M Bis-Tris pH5.7, 0.3M NaCl, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.35	α = 90
b = 85.96	β = 102.02
c = 77.33	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	173	CCD	ADSC QUANTUM 315r	mirrors	2013-01-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.92	Diamond	I04

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	2.12	37.82	97.9	0.061	0.07	2	4.1	54454	54303	2.6	2.6	32

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	2.16	37.81	99.2		0.572	0.65	2.6	4.3	7984

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	4IDX	2.12	37.4	2	54303	51526	2755	97.7	0.266	0.26548	0.26449	0.28	0.28348	0.3	RANDOM	19.666

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]
-2.87		0.56	-2.79		5.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.468
r_sphericity_free	31.054
r_dihedral_angle_3_deg	19.41
r_dihedral_angle_4_deg	16.765
r_dihedral_angle_1_deg	7.318
r_sphericity_bonded	3.41
r_rigid_bond_restr	2.654
r_angle_refined_deg	1.303
r_angle_other_deg	0.914
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.468
r_sphericity_free	31.054
r_dihedral_angle_3_deg	19.41
r_dihedral_angle_4_deg	16.765
r_dihedral_angle_1_deg	7.318
r_sphericity_bonded	3.41
r_rigid_bond_restr	2.654
r_angle_refined_deg	1.303
r_angle_other_deg	0.914
r_chiral_restr	0.08
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7035
Nucleic Acid Atoms	840
Solvent Atoms	163
Heterogen Atoms

Software

Software
Software Name	Purpose
iMOSFLM	data reduction
PHASER	phasing
REFMAC	refinement
SCALA	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.