Experiment: 3SIX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HHC	PDB ENTRY 2HHC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	350 mM potassium sodium tartrate 100 mM MES pH 6.5 50 mM MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.8	α = 90
b = 128.8	β = 90
c = 91.1	γ = 120

Symmetry
Space Group	P 65 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	MARMOSAIC 225 mm CCD		2011-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	0.97242	APS	22-BM

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	2.35	50	99.9	0.091	20.5	10.6	19194	19190		-3	56.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43	100		0.656	3.3	10.1	1878

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	R-FREE	PDB ENTRY 2HHC	2.35	50	19194	19048	1030	99.3	0.2124	0.2124	0.21	0.2569	RANDOM	56

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]
-0.6	-0.3		-0.6		0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.448
r_dihedral_angle_4_deg	18.094
r_dihedral_angle_3_deg	15.493
r_scangle_it	6.279
r_dihedral_angle_1_deg	5.978
r_scbond_it	4.203
r_mcangle_it	1.671
r_angle_refined_deg	1.491
r_angle_other_deg	0.876
r_mcbond_it	0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.448
r_dihedral_angle_4_deg	18.094
r_dihedral_angle_3_deg	15.493
r_scangle_it	6.279
r_dihedral_angle_1_deg	5.978
r_scbond_it	4.203
r_mcangle_it	1.671
r_angle_refined_deg	1.491
r_angle_other_deg	0.876
r_mcbond_it	0.86
r_mcbond_other	0.169
r_chiral_restr	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2345
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-3000	data reduction
HKL-3000	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 R01GM157729.