Experiment: 5K8D

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R7E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.3	297	5% Ethanol, 100mM TRIS pH 7.3

Crystal Properties
Matthews coefficient	Solvent content
4.61	73.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.295	α = 90
b = 136.295	β = 90
c = 365.098	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	MARMOSAIC 225 mm CCD		2012-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9792	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	4.2	50	99.8	0.174	0.181	0.054	4.7	13.8		26141

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4.2	4.27	100		0.471	0.855		12.6	1281

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	2R7E	4.19	37.6	24550	1309	98.77	0.3011	0.298	0.3619	RANDOM	205.935

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]
1.33			1.33		-2.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.592
r_dihedral_angle_3_deg	24.927
r_dihedral_angle_4_deg	22.016
r_scbond_it	18.193
r_mcangle_it	17.073
r_mcbond_it	10.221
r_dihedral_angle_1_deg	9.009
r_angle_refined_deg	1.896
r_chiral_restr	0.124
r_bond_refined_d	0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.592
r_dihedral_angle_3_deg	24.927
r_dihedral_angle_4_deg	22.016
r_scbond_it	18.193
r_mcangle_it	17.073
r_mcbond_it	10.221
r_dihedral_angle_1_deg	9.009
r_angle_refined_deg	1.896
r_chiral_restr	0.124
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9973
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	166

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	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 R01GM133198.