Experiment: 4DNE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MK5	PDB entry 1MK5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	10 mM MgSO4, 50 mM Na caodylate, 2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.72	α = 90
b = 93.782	β = 90
c = 104.413	γ = 90

Symmetry
Space Group	I 2 2 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		2009-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9334	ESRF	ID14-1

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	1.88	50	99.5	0.121		6.1	19193	19097			12.5

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	1.88	1.98	96.7		0.41

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 1MK5	1.88	46.86	18230	18119	966	99.39	0.18323	0.18323	0.18141	0.21897	RANDOM	15.225

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]
0.53			0.01		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.774
r_dihedral_angle_4_deg	13.899
r_dihedral_angle_3_deg	12.371
r_dihedral_angle_1_deg	6.935
r_scangle_it	2.782
r_scbond_it	1.857
r_mcangle_it	1.397
r_angle_refined_deg	1.382
r_mcbond_it	0.765
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.774
r_dihedral_angle_4_deg	13.899
r_dihedral_angle_3_deg	12.371
r_dihedral_angle_1_deg	6.935
r_scangle_it	2.782
r_scbond_it	1.857
r_mcangle_it	1.397
r_angle_refined_deg	1.382
r_mcbond_it	0.765
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1809
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	60

Software

Software
Software Name	Purpose
MxCuBE	data collection
MERLOT	phasing
REFMAC	refinement
XDS	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.