Experiment: 3CBK

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	291	0.14M ammonium fluoride, 14% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.066	α = 90
b = 85.066	β = 90
c = 115.691	γ = 90

Symmetry
Space Group	P 42 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	MAR CCD 165 mm	monochromator, multilayer mirror	2007-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.041	MAX II	I911-2

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	2.67	68.52	94.4	0.109	15	5.7	12662	11903		-3	69.27

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	2.67	2.77	96.5		0.576	2.1	5	1266

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	PDB ENTRY 3CBJ	2.67	20	-3	12662	11311	573	94.12	0.19543	0.19311	0.24232	RANDOM	52.476

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]
1.39			1.39		-2.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.414
r_dihedral_angle_3_deg	22.79
r_dihedral_angle_4_deg	20.704
r_dihedral_angle_1_deg	9.084
r_scangle_it	3.743
r_scbond_it	2.494
r_angle_refined_deg	2.357
r_mcangle_it	1.608
r_mcbond_it	0.956
r_symmetry_hbond_refined	0.418

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.414
r_dihedral_angle_3_deg	22.79
r_dihedral_angle_4_deg	20.704
r_dihedral_angle_1_deg	9.084
r_scangle_it	3.743
r_scbond_it	2.494
r_angle_refined_deg	2.357
r_mcangle_it	1.608
r_mcbond_it	0.956
r_symmetry_hbond_refined	0.418
r_symmetry_vdw_refined	0.358
r_nbtor_refined	0.334
r_nbd_refined	0.264
r_xyhbond_nbd_refined	0.253
r_chiral_restr	0.156
r_bond_refined_d	0.024
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2820
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	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.