Experiment: 3EF6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D7Y	pdb entry: 1D7Y including all side chains

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	286	0.1 M Tris pH 8.5, 1.5 M (NH)4SO 2 and 12% (v/v) glycerol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 286K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.128	α = 90
b = 77.128	β = 90
c = 156.372	γ = 90

Symmetry
Space Group	P 41 21 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	ADSC QUANTUM 210		2004-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.0332	NSLS	X6A

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	1.8	19.86	99	0.076		9.24		44352	1	1

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	1.8	1.86	96.4		0.386	4	7.04	4216

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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry: 1D7Y including all side chains	1.8	20	44198	44198	2229	99.28	0.205	0.205	0.203	0.243	RANDOM	28.002

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]
1.09			1.09		-2.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.31
r_dihedral_angle_4_deg	17.776
r_dihedral_angle_3_deg	13.779
r_dihedral_angle_1_deg	5.622
r_scangle_it	3.389
r_scbond_it	2.071
r_angle_refined_deg	1.521
r_mcangle_it	1.299
r_mcbond_it	0.86
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.31
r_dihedral_angle_4_deg	17.776
r_dihedral_angle_3_deg	13.779
r_dihedral_angle_1_deg	5.622
r_scangle_it	3.389
r_scbond_it	2.071
r_angle_refined_deg	1.521
r_mcangle_it	1.299
r_mcbond_it	0.86
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.195
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2940
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	105

Software

Software
Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
d*TREK	data reduction

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.