Experiment: 2NNR

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	1.5M Lithium Sulfate, 0.1M Hepes pH 8.5, protein concentration 8 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.546	α = 90
b = 49.546	β = 90
c = 187.576	γ = 120

Symmetry
Space Group	P 31 1 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	MAR CCD 165 mm		2005-01-25	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	MAR CCD 165 mm		2005-10-18	M	MAD
3	1
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8123	EMBL/DESY, HAMBURG	X11
2	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.9792, 0.9797, 0.9763	EMBL/DESY, HAMBURG	BW7A

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	1.7	62.5	99.6	0.038	38.3	7.8	29552	29434			31.888

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)
1,2	1.7	1.73	100		0.444	4	7.2	1435

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.7	45	29559	29404	1218	99.48	0.188	0.187	0.186	0.216	RANDOM	42.594

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]
0.91	0.46		0.91		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.127
r_dihedral_angle_3_deg	14.302
r_dihedral_angle_4_deg	9.273
r_dihedral_angle_1_deg	6.469
r_scangle_it	3.543
r_scbond_it	2.364
r_angle_refined_deg	1.538
r_mcangle_it	1.525
r_mcbond_it	0.999
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.127
r_dihedral_angle_3_deg	14.302
r_dihedral_angle_4_deg	9.273
r_dihedral_angle_1_deg	6.469
r_scangle_it	3.543
r_scbond_it	2.364
r_angle_refined_deg	1.538
r_mcangle_it	1.525
r_mcbond_it	0.999
r_nbtor_refined	0.31
r_xyhbond_nbd_refined	0.22
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.191
r_symmetry_vdw_refined	0.189
r_chiral_restr	0.119
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1702
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	48

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.