2P0A | pdb_00002p0a

The crystal structure of human synapsin III (SYN3) in complex with AMPPNP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I7L	Swissmodel based on PDB entries: 1I7L, 1I7N, 1PK8
experimental model	PDB	1I7N	Swissmodel based on PDB entries: 1I7L, 1I7N, 1PK8
experimental model	PDB	1PK8	Swissmodel based on PDB entries: 1I7L, 1I7N, 1PK8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	1.26M (NH4)2SO4, 0.2M Li2SO4, Tris-HCl pH 8.5, 20 % Ethylene glycol added as cryoprotectant, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.796	α = 90
b = 73.186	β = 100.74
c = 78.398	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	100	CCD	MARMOSAIC 225 mm CCD		2006-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99991	SLS	X10SA

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	1.9	64.28	99.2	0.132		3.5	56940	56940

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	1.9	2	94.4		0.477		2.3

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	Swissmodel based on PDB entries: 1I7L, 1I7N, 1PK8	1.9	47	54131	54131	2801	99.15	0.18311	0.18311	0.18131	0.19	0.21804	0.22	RANDOM	19.433

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]
-0.93		0.57	0.75		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.633
r_dihedral_angle_4_deg	19.816
r_dihedral_angle_3_deg	13.094
r_dihedral_angle_1_deg	6.23
r_scangle_it	2.419
r_scbond_it	1.703
r_angle_refined_deg	1.358
r_mcangle_it	1.01
r_angle_other_deg	0.882
r_mcbond_it	0.741
r_symmetry_vdw_refined	0.237
r_nbd_refined	0.192
r_nbd_other	0.19
r_symmetry_vdw_other	0.183
r_nbtor_refined	0.177
r_mcbond_other	0.171
r_xyhbond_nbd_refined	0.161
r_symmetry_hbond_refined	0.159
r_nbtor_other	0.085
r_chiral_restr	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4651
Nucleic Acid Atoms
Solvent Atoms	446
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing