6THJ

CBDP35 Native structure

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6S3Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298.5	4M Sodium Formate

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 332.51	α = 90
b = 94.59	β = 90.4
c = 83.19	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS 6M		2013-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.99988	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	37.88	99.6	0.186	0.993	6.8	6.3		130198

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.279	99.2		0.996	0.686	1.9	6.6

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	6S3Y	2.2	37.88	123766	6428	99.46	0.1983	0.1962	0.2384	RANDOM	31.326

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]
-2.91		1.03	1.5		1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.513
r_dihedral_angle_3_deg	16.759
r_dihedral_angle_4_deg	11.734
r_dihedral_angle_1_deg	7.339
r_angle_refined_deg	1.602
r_angle_other_deg	1.263
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.513
r_dihedral_angle_3_deg	16.759
r_dihedral_angle_4_deg	11.734
r_dihedral_angle_1_deg	7.339
r_angle_refined_deg	1.602
r_angle_other_deg	1.263
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13570
Nucleic Acid Atoms
Solvent Atoms	1288
Heterogen Atoms	315

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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.