Experiment: 2GNN

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	0.6 M Ammonium sulfate, 3% PEG 4K, 0.1 M Sodium citrate, 0.3% Benzamidine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
5.10419	75.902153

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.6	α = 90
b = 98.6	β = 90
c = 240	γ = 90

Symmetry
Space Group	P 41 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	MAR CCD 165 mm		2004-07-27	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MAR CCD 165 mm		2004-07-31	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00017	SLS	X06SA
2	SYNCHROTRON	SLS BEAMLINE X06SA	1.698383	SLS	X06SA

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	2.3	48.48	93.4	0.081	14.58			52820			57.637

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	2.3	2.4	98.4	85.4	0.799	3.1		6199

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.3	48.48	52820	2687	98.66	0.224	0.224	0.223	0.247	RANDOM	66.047

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]
1.93			1.93		-3.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.619
r_dihedral_angle_3_deg	15.601
r_dihedral_angle_4_deg	12.628
r_scangle_it	7.725
r_scbond_it	5.293
r_dihedral_angle_1_deg	5.052
r_mcangle_it	3.347
r_mcbond_it	2.075
r_angle_refined_deg	1.25
r_nbtor_refined	0.293

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.619
r_dihedral_angle_3_deg	15.601
r_dihedral_angle_4_deg	12.628
r_scangle_it	7.725
r_scbond_it	5.293
r_dihedral_angle_1_deg	5.052
r_mcangle_it	3.347
r_mcbond_it	2.075
r_angle_refined_deg	1.25
r_nbtor_refined	0.293
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.198
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.071
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2831
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	132

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
SHELXD	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.