Experiment: 3CEK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QKR	PDB entries 2QKR, 2H9V, 2F2U, 2EUE
experimental model	PDB	2H9V	PDB entries 2QKR, 2H9V, 2F2U, 2EUE
experimental model	PDB	2F2U	PDB entries 2QKR, 2H9V, 2F2U, 2EUE
experimental model	PDB	2EUE	PDB entries 2QKR, 2H9V, 2F2U, 2EUE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	277	55% PEG 300, 0.25M NaCl, Na/K Phosphate pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.846	α = 90
b = 107.467	β = 90
c = 111.872	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	MARMOSAIC 225 mm CCD		2007-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97912	SLS	X10SA

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	40.456	99.8	0.084	0.084	17.1	10.8	19092	19054

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	2.42	99.1		0.898	2.5	9.3	2722

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 entries 2QKR, 2H9V, 2F2U, 2EUE	2.3	34	19053	19053	980	99.85	0.188	0.188	0.184	0.25	RANDOM	44.156

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]
-2.35			2.8		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.339
r_dihedral_angle_4_deg	25.939
r_dihedral_angle_3_deg	15.097
r_scangle_it	8.408
r_dihedral_angle_1_deg	6.465
r_scbond_it	6.184
r_mcangle_it	3.771
r_mcbond_it	2.266
r_angle_refined_deg	1.472
r_angle_other_deg	0.946

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.339
r_dihedral_angle_4_deg	25.939
r_dihedral_angle_3_deg	15.097
r_scangle_it	8.408
r_dihedral_angle_1_deg	6.465
r_scbond_it	6.184
r_mcangle_it	3.771
r_mcbond_it	2.266
r_angle_refined_deg	1.472
r_angle_other_deg	0.946
r_mcbond_other	0.592
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2031
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	32

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	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.