3F01 | pdb_00003f01

Crystal Structure of Synaptotagmin I C2A domain with Cu(II)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F00	PDB entry 3F00

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	2.0M Li2SO4, 100mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.088	α = 90
b = 38.561	β = 97.35
c = 44.267	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	CCD	SBC-3		2008-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.379	APS	19-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	1.7	50	99.4	0.05	54.378	5.3		15627

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)
	1.7	1.73	97.4		0.164		4.5	1484

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 (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 3F00	1.7	28.98	15625	779	99.57	0.195	0.193	0.19	0.229	0.22	RANDOM	20.386

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.468
r_dihedral_angle_3_deg	9.531
r_dihedral_angle_4_deg	5.364
r_sphericity_free	4.056
r_dihedral_angle_1_deg	3.903
r_sphericity_bonded	3.864
r_mcangle_it	2.332
r_scangle_it	1.955
r_mcbond_it	1.571
r_scbond_it	1.382
r_angle_refined_deg	1.351
r_rigid_bond_restr	1.323
r_nbtor_refined	0.32
r_nbd_refined	0.266
r_symmetry_vdw_refined	0.236
r_symmetry_hbond_refined	0.212
r_xyhbond_nbd_refined	0.198
r_metal_ion_refined	0.194
r_chiral_restr	0.097
r_bond_refined_d	0.018
r_symmetry_metal_ion_refined	0.011
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1150
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling