Experiment: 5CKL

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S6A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.8	277.15	10 mM Tris pH 7.8, 100 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.333	α = 90
b = 50.538	β = 90
c = 130.136	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2013-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.8000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	0.99	65.07	99.6	0.032	0.013	1	28.3	6.5		129938

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.99	1.01	97.4		0.611	0.258	0.83	3.3	6.3	6218

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3s6a	0.99	65.07	123331	6534	99.46	0.1127	0.1121	0.11	0.1246	0.12	RANDOM	12.635

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]
-0.09			-0.19		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.905
r_dihedral_angle_2_deg	34.806
r_dihedral_angle_4_deg	15.745
r_sphericity_bonded	13.638
r_dihedral_angle_3_deg	11.918
r_rigid_bond_restr	7.738
r_dihedral_angle_1_deg	5.225
r_angle_refined_deg	2.2
r_mcangle_it	2.099
r_mcbond_it	1.899

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.905
r_dihedral_angle_2_deg	34.806
r_dihedral_angle_4_deg	15.745
r_sphericity_bonded	13.638
r_dihedral_angle_3_deg	11.918
r_rigid_bond_restr	7.738
r_dihedral_angle_1_deg	5.225
r_angle_refined_deg	2.2
r_mcangle_it	2.099
r_mcbond_it	1.899
r_mcbond_other	1.558
r_angle_other_deg	1.111
r_chiral_restr	0.156
r_bond_refined_d	0.029
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1498
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	9

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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.