Experiment: 3KBC

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NWX	PDB entry 2NWX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	277	PEG MME 350, CaCl2, MES, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.46	72.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.142	α = 90
b = 206.78	β = 90
c = 205.971	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 315		2008-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.000	NSLS	X25

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	3.5	40	97.9	0.118	6.1	8.3	30570	29928			109.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.5	3.63	92.2			6.4	2776

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2NWX	3.51	12	29864	28969	1473	97.22	0.267	0.267	0.27	RANDOM	100.882

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]
5.25			2.99		-8.24

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.288
r_dihedral_angle_2_deg	0.881
r_dihedral_angle_3_deg	0.752
r_dihedral_angle_4_deg	0.549
r_scangle_it	0.514
r_scbond_it	0.282
r_mcangle_it	0.226
r_mcbond_it	0.118
r_dihedral_angle_1_deg	0.097
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.288
r_dihedral_angle_2_deg	0.881
r_dihedral_angle_3_deg	0.752
r_dihedral_angle_4_deg	0.549
r_scangle_it	0.514
r_scbond_it	0.282
r_mcangle_it	0.226
r_mcbond_it	0.118
r_dihedral_angle_1_deg	0.097
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9060
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	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.