Experiment: 3EYL

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CLX	PDB entry 3clx

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	293	Mg formate, pH 5.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.423	α = 90
b = 170.423	β = 90
c = 170.423	γ = 90

Symmetry
Space Group	I 41 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	100	CCD	ADSC QUANTUM 315		2008-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.013	ESRF	ID23-1

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	3	40	99.7	0.092	20.9	11.6		8740

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	3	3.16	100		0.667	3.7	12	1253

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3clx	3	38.11	8740	8303	414	99.45	0.19111	0.1888	0.23877	RANDOM	50.602

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.586
r_dihedral_angle_3_deg	19.616
r_dihedral_angle_4_deg	17.366
r_scangle_it	5.065
r_dihedral_angle_1_deg	4.647
r_scbond_it	3.101
r_mcangle_it	2.326
r_mcbond_it	1.299
r_angle_refined_deg	1.066
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.586
r_dihedral_angle_3_deg	19.616
r_dihedral_angle_4_deg	17.366
r_scangle_it	5.065
r_dihedral_angle_1_deg	4.647
r_scbond_it	3.101
r_mcangle_it	2.326
r_mcbond_it	1.299
r_angle_refined_deg	1.066
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.248
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.087
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1638
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	76

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.