Experiment: 3BMX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EX1	PDB entries: 1EX1, 1IIX, 1J8V, 1LQ2, 1X38
experimental model	PDB	1IIX	PDB entries: 1EX1, 1IIX, 1J8V, 1LQ2, 1X38
experimental model	PDB	1J8V	PDB entries: 1EX1, 1IIX, 1J8V, 1LQ2, 1X38
experimental model	PDB	1LQ2	PDB entries: 1EX1, 1IIX, 1J8V, 1LQ2, 1X38
experimental model	PDB	1X38	PDB entries: 1EX1, 1IIX, 1J8V, 1LQ2, 1X38

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.9	291	0.1M sodium acetate, 30-33 % PEG 1000, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.385	α = 79.79
b = 73.085	β = 69.61
c = 83.567	γ = 88.25

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	PIXEL	PSI PILATUS 6M		2007-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99989	SLS	X06SA

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	1.4	43	90.8	0.084	13.25	7	227962	227962		-3	20.9

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	1.4	1.5	53.7		0.605	2.65	2.66	25215

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 entries: 1EX1, 1IIX, 1J8V, 1LQ2, 1X38	1.4	42.835	1.99	227962	11453	90.85	0.129	0.127	0.166	random	18.81

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]
2.262	-5.86	2.47	-1.195	-2.03	-1.251

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.054
f_angle_d	0.967
f_chiral_restr	0.216
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9526
Nucleic Acid Atoms
Solvent Atoms	1388
Heterogen Atoms	65

Software

Software
Software Name	Purpose
PHENIX	refinement
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
BUCCANEER	phasing
ARP/wARP	model building
RESOLVE	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.