Experiment: 5DSD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4QB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	Crystallization solution: 1.33 M LiSO4, 0.1 M Tris pH 8.5. 1:1 ratio (250 nL: 250 nL) of precipitant to protein (at a concentration of 13.9 mg/ml). 60 mcL reservoir. Protein purification buffer 50mM Tris-HCl, 150 mM NaCl; pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
5.94	79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.957	α = 90
b = 108.957	β = 90
c = 82.736	γ = 120

Symmetry
Space Group	P 64 2 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	CCD	RAYONIX MX300HE		2014-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.99	APS	21-ID-D

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	2.3	80	94.3	0.084	20.3	14.8		12398

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	2.3	2.38	64.7		0.432	0.432	1.9	7.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4QB0	2.31	80	11792	604	94.04	0.1692	0.1676	0.18	0.2025	0.21	RANDOM	81.78

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]
0.68	0.34		0.68		-2.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.102
r_mcangle_it	14.363
r_mcbond_it	13.696
r_mcbond_other	13.629
r_dihedral_angle_3_deg	13.36
r_dihedral_angle_4_deg	10.807
r_dihedral_angle_1_deg	5.678
r_angle_refined_deg	1.253
r_angle_other_deg	0.899
r_chiral_restr	0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.102
r_mcangle_it	14.363
r_mcbond_it	13.696
r_mcbond_other	13.629
r_dihedral_angle_3_deg	13.36
r_dihedral_angle_4_deg	10.807
r_dihedral_angle_1_deg	5.678
r_angle_refined_deg	1.253
r_angle_other_deg	0.899
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	861
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	13

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	phasing
SCALEPACK	data scaling
PHENIX	model building
HKL-3000	data reduction
Coot	model building

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.