Experiment: 1PK8

Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.ATP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AUX	PDB ENTRY 1AUX, ATPgammaS and Ca2+ removed

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	299	PEGMME 5000, Tris, NaCl, Ca.ATP, EDTA, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.6	α = 80.6
b = 78.4	β = 76.9
c = 135	γ = 71.8

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	CUSTOM-MADE		2000-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.008	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	40	96.3	0.058	20.9	3.7		150398			19

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.18	92		0.373	2.8	3.6	14381

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1AUX, ATPgammaS and Ca2+ removed	2.1	20	149733	142899	14256	91.9	0.235	0.222	0.222	0.2318	0.259	0.2667	random	34.2

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]
4.03	1.83	-0.7	0.74	-0.42	-4.78

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.3
c_angle_deg	1.3
c_improper_angle_d	0.5
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18531
Nucleic Acid Atoms
Solvent Atoms	665
Heterogen Atoms	512

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement
HKL-2000	data reduction