3Q9C | pdb_00003q9c

Crystal Structure of H159A APAH complexed with N8-acetylspermidine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q9F	PDB ENTRY 3Q9F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	1.0 M sodium phosphate, 0.8 M potassium phosphate, 0.2 M lithium sulfate, 0.1 M CAPS pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.461	α = 98.47
b = 120.154	β = 94.41
c = 118.448	γ = 115.89

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 315r	Kirpatrick Baez focusing mirrors	2010-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97949	APS	24-ID-C

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	2.3	50	86.9	0.109	0.109	7.472	2.4	252823	219596		-3

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)
	2.3	2.37	96.9		0.361	0.361	2.059	2.3	21913

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3Q9F	2.3	50	252823	219596	21958	86.9	0.1859	0.1859	0.1859	0.18	0.2271	0.22	random	25.677

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]
3.189	0.925	-3.878	0.083	2.709	-3.272

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.918
c_scbond_it	1.975
c_mcangle_it	1.748
c_angle_deg	1.217
c_mcbond_it	1.109
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	30756
Nucleic Acid Atoms
Solvent Atoms	1752
Heterogen Atoms	192

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
APS-24IDC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	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.