Experiment: 3APD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E8Y	PDB ENTRY 1E8Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	20% PEG3350, 0.2M (NH4)2SO4, 0.1M Tris-HCl, streak seeding, pH 7.2, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.95	α = 90
b = 67.46	β = 95.68
c = 106.28	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 315	mirrors	2006-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

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	2.548	60.953	99.7	0.046	0.046	17.7	3.7	33084	33084

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)
	2.55	2.61	99.41		0.68		3.76	2419

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	PDB ENTRY 1E8Y	2.55	60.95	33084	1675	100	0.2532	0.2498	0.3162	RANDOM	59.4382

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]
-0.88		1.2	2.6		-1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.638
r_dihedral_angle_3_deg	16.247
r_dihedral_angle_4_deg	13.451
r_dihedral_angle_1_deg	6.21
r_scangle_it	6.181
r_scbond_it	4.191
r_mcangle_it	3.074
r_mcbond_it	1.74
r_angle_refined_deg	1.08
r_angle_other_deg	0.801

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.638
r_dihedral_angle_3_deg	16.247
r_dihedral_angle_4_deg	13.451
r_dihedral_angle_1_deg	6.21
r_scangle_it	6.181
r_scbond_it	4.191
r_mcangle_it	3.074
r_mcbond_it	1.74
r_angle_refined_deg	1.08
r_angle_other_deg	0.801
r_mcbond_other	0.355
r_chiral_restr	0.06
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	6562
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	38

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
MOLREP	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.