Experiment: 3BL8

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.8	293	3.5% PEG 6000, 0.1M Bicine, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 214.723	α = 90
b = 92.567	β = 98.36
c = 188.408	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MAR CCD 165 mm		2007-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.9793	NSLS	X4C

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	3.3	30	98.6	0.101	7.9	3.1	57279	54385

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	3.3	3.42	96.9		0.503	0.503	1.4	2.8	5279

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	3.3	20	54279	54190	2714	98.51	0.221	0.219	0.262	RANDOM	126.202

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]
1.45		-9.25	-2.62		-1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.639
r_dihedral_angle_3_deg	19.917
r_dihedral_angle_4_deg	16.001
r_dihedral_angle_1_deg	6.05
r_angle_refined_deg	1.213
r_scangle_it	0.937
r_scbond_it	0.528
r_mcangle_it	0.51
r_nbtor_refined	0.309
r_mcbond_it	0.278

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.639
r_dihedral_angle_3_deg	19.917
r_dihedral_angle_4_deg	16.001
r_dihedral_angle_1_deg	6.05
r_angle_refined_deg	1.213
r_scangle_it	0.937
r_scbond_it	0.528
r_mcangle_it	0.51
r_nbtor_refined	0.309
r_mcbond_it	0.278
r_symmetry_vdw_refined	0.213
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.106
r_chiral_restr	0.086
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17172
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	150

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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.