Experiment: 4DBM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BYN	2BYN, 2PGZ, 2BYP, 2BYR, 2BYS, 3C79
experimental model	PDB	2PGZ	2BYN, 2PGZ, 2BYP, 2BYR, 2BYS, 3C79
experimental model	PDB	2BYP	2BYN, 2PGZ, 2BYP, 2BYR, 2BYS, 3C79
experimental model	PDB	2BYR	2BYN, 2PGZ, 2BYP, 2BYR, 2BYS, 3C79
experimental model	PDB	2BYS	2BYN, 2PGZ, 2BYP, 2BYR, 2BYS, 3C79
experimental model	PDB	3C79	2BYN, 2PGZ, 2BYP, 2BYR, 2BYS, 3C79

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	295	0.1M Tris-HCl, 0.25M magnesium chloride, 12% (w/v) PEG 4000, 10% (v/v) glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.338	α = 90
b = 115.097	β = 90
c = 131.379	γ = 90

Symmetry
Space Group	P 21 21 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 315r		2008-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2		ALS	8.2.2

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	50	98.5	0.075	0.075	28	8		59275		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	94.9		0.473	0.473	2.556	6.6	2805

Refinement

Statistics
Diffraction ID	Structure Solution 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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2BYN, 2PGZ, 2BYP, 2BYR, 2BYS, 3C79	2.3	43.29	57215	57215	1939	95.04	0.1962	0.1942	0.2518	36.15

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]
7.2287			-6.7385		-0.4902

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.484
f_angle_d	1.185
f_chiral_restr	0.085
f_bond_d	0.013
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8357
Nucleic Acid Atoms
Solvent Atoms	458
Heterogen Atoms	220

Software

Software
Software Name	Purpose
HKL-2000	data collection
ccp4:	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4:	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 R01GM133198.