1TJM

Crystallographic Identification of Sr2+ Coordination Site in Synaptotagmin I C2B Domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K5W	pdb entry 1K5W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	277	ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.644	α = 90
b = 54.644	β = 90
c = 103.317	γ = 120

Symmetry
Space Group	P 32 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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

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	1.18	20	95.5	0.048	31.1	10.9		56844

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	1.18	1.2	56.2		0.19	3.4

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 1K5W	1.18	20	53935	2861	95.47	0.15897	0.15818	0.17373	RANDOM	13.474

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]
-0.49	-0.25		-0.49		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.39
r_sphericity_free	5.062
r_scangle_it	5.041
r_sphericity_bonded	3.955
r_scbond_it	3.201
r_mcangle_it	2.627
r_rigid_bond_restr	1.721
r_angle_refined_deg	1.71
r_mcbond_it	1.702
r_angle_other_deg	0.912
r_symmetry_vdw_other	0.277
r_nbd_other	0.251
r_nbd_refined	0.244
r_symmetry_vdw_refined	0.195
r_metal_ion_refined	0.192
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.099
r_symmetry_hbond_refined	0.092
r_nbtor_other	0.087
r_gen_planes_other	0.02
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1228
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing