Experiment: 3NIM

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	0.04M sodium cacodylate trihydrate pH 6.0, 0.04M magnesium acetate tetrahydrate, 30%(v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.868	α = 90
b = 44.868	β = 90
c = 140.136	γ = 120

Symmetry
Space Group	P 32

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		2009-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	50	92.8	0.08	12.4	4.9		19874

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	2.07	91.3		0.596		5.1	1930

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	22.73	19825	1039	92.76	0.1932	0.1906	0.24	RANDOM	39.8407

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.502
r_dihedral_angle_3_deg	15.185
r_dihedral_angle_4_deg	14.507
r_dihedral_angle_1_deg	5.647
r_scangle_it	2.53
r_scbond_it	1.591
r_mcangle_it	1.453
r_angle_refined_deg	1.211
r_mcbond_it	0.843
r_nbtor_refined	0.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.502
r_dihedral_angle_3_deg	15.185
r_dihedral_angle_4_deg	14.507
r_dihedral_angle_1_deg	5.647
r_scangle_it	2.53
r_scbond_it	1.591
r_mcangle_it	1.453
r_angle_refined_deg	1.211
r_mcbond_it	0.843
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.241
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.079
r_metal_ion_refined	0.028
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2571
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	12

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.