Experiment: 2EFD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	289	3% PEG4000, 50mM imidazole malate, 50mM NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 189.544	α = 90
b = 189.544	β = 90
c = 75.17	γ = 120

Symmetry
Space Group	P 61

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		2005-04-23	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2005-04-23	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.91980	Photon Factory	AR-NW12A
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97920, 0.91162, 0.97932	SSRL	BL9-2

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	3	100	96.1	0.091	0.091	27.6	11.2		29805	1	1	100.3

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	3	3.11	100		0.633	3.5	10.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	3	38.95	28248	1494	95.89	0.30797	0.30576	0.35126	RANDOM	74.663

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]
1.44	0.72		1.44		-2.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.359
r_dihedral_angle_3_deg	19.967
r_dihedral_angle_4_deg	18.955
r_dihedral_angle_1_deg	5.685
r_scangle_it	1.273
r_angle_refined_deg	1.2
r_mcangle_it	0.765
r_scbond_it	0.745
r_mcbond_it	0.428
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.359
r_dihedral_angle_3_deg	19.967
r_dihedral_angle_4_deg	18.955
r_dihedral_angle_1_deg	5.685
r_scangle_it	1.273
r_angle_refined_deg	1.2
r_mcangle_it	0.765
r_scbond_it	0.745
r_mcbond_it	0.428
r_nbtor_refined	0.303
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.224
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.085
r_symmetry_hbond_refined	0.024
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6266
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	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.