Experiment: 5DQF

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	1 ul of 30 mg/mL protein in 10 mM Tris pH 7.5, 150 mM NaCl was mixed with 1ul of the well condition: 100 mM Tris pH 7.5, 1800 mM (NH4)2SO4, 87.5 mM NaBr, 2.5% w/v PEG 8K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.234	α = 90
b = 94.234	β = 90
c = 141.893	γ = 120

Symmetry
Space Group	P 61

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	MARMOSAIC 300 mm CCD	Bimorph K-B pair	2011-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.979	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.15	80	99.8	0.07	0.07	0.073	0.027	9.7	7.7		38645			43

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	100		0.947	0.363	0.785		7.7	1923

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	3V08	2.15	80	36754	1879	99.79	0.1912	0.1888	0.2407	RANDOM	55.868

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]
1.55	0.78		1.55		-5.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.701
r_dihedral_angle_4_deg	17.921
r_dihedral_angle_3_deg	13.551
r_dihedral_angle_1_deg	5.021
r_mcangle_it	2.101
r_angle_refined_deg	1.401
r_mcbond_it	1.325
r_mcbond_other	1.325
r_angle_other_deg	1.014
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.701
r_dihedral_angle_4_deg	17.921
r_dihedral_angle_3_deg	13.551
r_dihedral_angle_1_deg	5.021
r_mcangle_it	2.101
r_angle_refined_deg	1.401
r_mcbond_it	1.325
r_mcbond_other	1.325
r_angle_other_deg	1.014
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4488
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	124

Software

Software
Software Name	Purpose
MD2	data collection
HKL-3000	data reduction
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

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.