Experiment: 3BX1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	0.1 M sodium acetate buffer pH 5.6 and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.637	α = 90
b = 100.637	β = 90
c = 216.242	γ = 90

Symmetry
Space Group	P 41 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	291	CCD	ADSC QUANTUM 315		2007-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.004	ESRF	ID23-1

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	1.85	50	87.7	0.105	0.076	16.3	4.3	95850	84089			27

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)
	1.85	1.92	41.4		0.471	0.415	1.6	1.6	3898

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 entries 1AVA and 1SVN	1.85	35.11	83612	79404	4208	87.3	0.20379	0.2019	0.23894	RANDOM	34.31

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]
0.81			0.81		-1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.832
r_dihedral_angle_4_deg	19.94
r_dihedral_angle_3_deg	18.222
r_dihedral_angle_1_deg	13.901
r_scangle_it	4.099
r_scbond_it	2.69
r_angle_refined_deg	1.915
r_mcangle_it	1.847
r_mcbond_it	1.039
r_symmetry_hbond_refined	0.335

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.832
r_dihedral_angle_4_deg	19.94
r_dihedral_angle_3_deg	18.222
r_dihedral_angle_1_deg	13.901
r_scangle_it	4.099
r_scbond_it	2.69
r_angle_refined_deg	1.915
r_mcangle_it	1.847
r_mcbond_it	1.039
r_symmetry_hbond_refined	0.335
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.287
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.165
r_metal_ion_refined	0.148
r_bond_refined_d	0.017
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6620
Nucleic Acid Atoms
Solvent Atoms	574
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	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 R01GM133198.