Experiment: 3D6N

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ML4	1xrtA, 1ml4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	3 mg/mL protein in 10mM Hepes, 10 mM sodium citrate, 2 mM DTT mixed 6:1 with 25% ethylene glycol, 10mM BaCL2 and equilibrated with same., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.439	α = 90
b = 158.439	β = 90
c = 233.553	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 270		2006-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	65	99.97	0.8	23.83	5.8	47628	47614			34.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	99.4		0.546	2.96	5.7	9768

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	SAD	THROUGHOUT	1xrtA, 1ml4	2.3	65	47628	47614	2544	99.97	0.1665	0.16646	0.16444	0.20404	RANDOM	34.423

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]
0.11	0.06		0.11		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.416
r_dihedral_angle_4_deg	21.933
r_dihedral_angle_3_deg	16.876
r_dihedral_angle_1_deg	8.984
r_scangle_it	4.502
r_scbond_it	2.926
r_angle_refined_deg	1.815
r_mcangle_it	1.665
r_mcbond_it	1.069
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.416
r_dihedral_angle_4_deg	21.933
r_dihedral_angle_3_deg	16.876
r_dihedral_angle_1_deg	8.984
r_scangle_it	4.502
r_scbond_it	2.926
r_angle_refined_deg	1.815
r_mcangle_it	1.665
r_mcbond_it	1.069
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.272
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.205
r_xyhbond_nbd_refined	0.204
r_chiral_restr	0.132
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5632
Nucleic Acid Atoms
Solvent Atoms	422
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	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.