Experiment: 3H9J

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H9G	PDB entry 3H9G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291.2	24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Na Hepes pH 7.5, 100 mM MgSO4, 9 mM AMPCPP, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.841	α = 90
b = 138.004	β = 92.21
c = 80.816	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	MAR scanner 300 mm plate	Rosenbaum-Rock vertical focusing mirror	2007-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97926	APS	22-ID

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	50	98.9	0.081	17.14	4.1	54611	54611			41.7

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	2.3	2.38	91.1		0.364		3.3	5027

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3H9G	2.3	39.97	54215	53753	2715	99.16	0.203	0.199	0.196	0.255	RANDOM	44.194

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]
0.73		-0.08	-1.57		0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.605
r_dihedral_angle_4_deg	19.488
r_dihedral_angle_3_deg	16.999
r_dihedral_angle_1_deg	5.873
r_scangle_it	1.972
r_angle_refined_deg	1.248
r_scbond_it	1.229
r_mcangle_it	0.912
r_mcbond_it	0.511
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.605
r_dihedral_angle_4_deg	19.488
r_dihedral_angle_3_deg	16.999
r_dihedral_angle_1_deg	5.873
r_scangle_it	1.972
r_angle_refined_deg	1.248
r_scbond_it	1.229
r_mcangle_it	0.912
r_mcbond_it	0.511
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.205
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.162
r_symmetry_hbond_refined	0.141
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10482
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	142

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
X-GEN	data scaling
HKL-2000	data reduction
REFMAC	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.