Experiment: 3NIJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NIS	PDB ENTRY 3NIS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	0.16M ammonium acetate, 0.01M calcium chloride dihydrate, 0.05M sodium cacodylate trihydrate pH 6.5, 8%(w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.323	α = 90
b = 58.323	β = 90
c = 111.22	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210		2009-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A	1.0000	PAL/PLS	4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	50	99.6	0.082	13.7	21		7022

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.18	100		0.522		20.6	673

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3NIS	2.1	23	6980	333	99.69	0.2631	0.2616	0.2941	RANDOM	63.926

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]
-0.03	-0.02		-0.03		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.45
r_dihedral_angle_3_deg	14.916
r_dihedral_angle_4_deg	14.288
r_dihedral_angle_1_deg	5.148
r_scangle_it	1.251
r_angle_refined_deg	0.935
r_scbond_it	0.8
r_mcangle_it	0.749
r_mcbond_it	0.426
r_symmetry_vdw_refined	0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.45
r_dihedral_angle_3_deg	14.916
r_dihedral_angle_4_deg	14.288
r_dihedral_angle_1_deg	5.148
r_scangle_it	1.251
r_angle_refined_deg	0.935
r_scbond_it	0.8
r_mcangle_it	0.749
r_mcbond_it	0.426
r_symmetry_vdw_refined	0.39
r_nbtor_refined	0.29
r_nbd_refined	0.177
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.079
r_metal_ion_refined	0.032
r_symmetry_hbond_refined	0.013
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	641
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	3

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

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.