Experiment: 1NAE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GMM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	291	26%PEG 4K, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.63	24.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.648	α = 90
b = 49.746	β = 93.18
c = 36.082	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARRESEARCH	long mirror focused	2002-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.05	36.04		0.07	0.07	12.4	2.3	6680	6382			20.33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.05	2.12			0.186	0.186	5.4	2.2	649

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1gmm	2.05	36.04	5544	279	87.34	0.13748	0.13748	0.1345	0.14	0.19487	0.21	RANDOM	19.907

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]
0.87		-0.1	-0.04		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.15
r_scangle_it	3.132
r_scbond_it	2.276
r_angle_refined_deg	1.528
r_mcangle_it	1.353
r_mcbond_it	0.771
r_symmetry_vdw_refined	0.223
r_symmetry_hbond_refined	0.214
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.144

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.15
r_scangle_it	3.132
r_scbond_it	2.276
r_angle_refined_deg	1.528
r_mcangle_it	1.353
r_mcbond_it	0.771
r_symmetry_vdw_refined	0.223
r_symmetry_hbond_refined	0.214
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.103
r_metal_ion_refined	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	952
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	29

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

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.