Experiment: 3CK4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B22	PDB ENTRY 2B22

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	0.1M Tris-HCl, 0.2M magnesium chloride, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.846	α = 115.77
b = 49.107	β = 94.21
c = 51.917	γ = 109.62

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2006-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.9786	NSLS	X4C

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	1.7	45.2	96.5	0.042	12.7	2	41918	41918			22.3

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)
	1.7	1.76	95.8		0.413	2.1	2	4137

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 2B22	1.7	45.18	41918	41918	2111	96.5	0.173	0.17305	0.17055	0.22062	RANDOM	30.554

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]
-0.66	-0.32		-0.19	0.05	0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.991
r_dihedral_angle_3_deg	16.093
r_dihedral_angle_4_deg	8.542
r_scangle_it	4.227
r_dihedral_angle_1_deg	3.886
r_scbond_it	2.668
r_angle_refined_deg	1.537
r_mcangle_it	1.453
r_mcbond_it	0.977
r_symmetry_vdw_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.991
r_dihedral_angle_3_deg	16.093
r_dihedral_angle_4_deg	8.542
r_scangle_it	4.227
r_dihedral_angle_1_deg	3.886
r_scbond_it	2.668
r_angle_refined_deg	1.537
r_mcangle_it	1.453
r_mcbond_it	0.977
r_symmetry_vdw_refined	0.311
r_nbtor_refined	0.303
r_nbd_refined	0.209
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.148
r_metal_ion_refined	0.11
r_chiral_restr	0.098
r_bond_refined_d	0.02
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3163
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

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.