Experiment: 2O8B

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	290	11% PEG 8000, 10 mM magnesium sulfate, 100 mM bis-tris-propane, pH 7, VAPOR DIFFUSION, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 258.74	α = 90
b = 258.74	β = 90
c = 258.74	γ = 90

Symmetry
Space Group	P 43 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 300 mm plate	mirrors	2003-03-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.0065, 0.9793, 0.9794, 0.9769	NSLS	X25

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	2.75	48.047	99.8	0.094	0.094	7.2	9.4	77245	76720		-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	2.75	2.82	97.9		0.504	0.504	1.5	5.6	5473

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	MAD	THROUGHOUT	2.75	20	76598	76483	3872	99.85	0.245	0.243	0.281	RANDOM	83.86

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.273
r_dihedral_angle_4_deg	13.912
r_dihedral_angle_3_deg	11.27
r_dihedral_angle_1_deg	2.478
r_angle_refined_deg	1.461
r_scangle_it	1.208
r_scbond_it	0.725
r_mcangle_it	0.597
r_mcbond_it	0.35
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.273
r_dihedral_angle_4_deg	13.912
r_dihedral_angle_3_deg	11.27
r_dihedral_angle_1_deg	2.478
r_angle_refined_deg	1.461
r_scangle_it	1.208
r_scbond_it	0.725
r_mcangle_it	0.597
r_mcbond_it	0.35
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.227
r_xyhbond_nbd_refined	0.184
r_nbd_refined	0.183
r_symmetry_vdw_refined	0.157
r_chiral_restr	0.101
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13983
Nucleic Acid Atoms	610
Solvent Atoms	43
Heterogen Atoms	56

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
CNS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.