Experiment: 3NIT

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	0.1M HEPES pH 7.7, 70%(v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.207	α = 90
b = 39.207	β = 90
c = 274.689	γ = 120

Symmetry
Space Group	P 65 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	IMAGE PLATE	MAC Science DIP-2030		2008-10-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6B	1.12713,1.28305,1.28325	PAL/PLS	6B

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	2.52	50	94.2	0.091	9.3	17.3		4701

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)
	2.52	2.61	54.2		0.711		6.4	264

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.6	31.84	4194	199	98.45	0.2457	0.2439	0.2841	RANDOM	68.843

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]
2.68	1.34		2.68		-4.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.855
r_dihedral_angle_3_deg	15.934
r_dihedral_angle_4_deg	7.315
r_dihedral_angle_1_deg	5.131
r_scangle_it	1.331
r_angle_refined_deg	0.934
r_mcangle_it	0.859
r_scbond_it	0.778
r_mcbond_it	0.476
r_nbtor_refined	0.287

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.855
r_dihedral_angle_3_deg	15.934
r_dihedral_angle_4_deg	7.315
r_dihedral_angle_1_deg	5.131
r_scangle_it	1.331
r_angle_refined_deg	0.934
r_mcangle_it	0.859
r_scbond_it	0.778
r_mcbond_it	0.476
r_nbtor_refined	0.287
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.154
r_xyhbond_nbd_refined	0.135
r_symmetry_hbond_refined	0.126
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	690
Nucleic Acid Atoms
Solvent Atoms	21
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
SOLVE	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 R01GM133198.