1TJX

Crystallographic Identification of Ca2+ Coordination Sites in Synaptotagmin I C2B Domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5	277	ammonium sulfate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.00

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.55	α = 90
b = 54.55	β = 90
c = 103.59	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		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	1.04	20	99	0.103	19.3	5.55		85544

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	1.04	1.06	96.6		0.416	1.62

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1K5W	1.04	19.5	85544	81211	4278	99	0.167	0.166	0.184	RANDOM	12.29

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]
-0.48	-0.24		-0.48		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.204
r_sphericity_free	4.943
r_scangle_it	4.75
r_sphericity_bonded	4.285
r_scbond_it	3.02
r_mcangle_it	2.672
r_mcbond_it	1.752
r_angle_refined_deg	1.714
r_rigid_bond_restr	1.675
r_angle_other_deg	1.433
r_symmetry_vdw_other	0.316
r_symmetry_vdw_refined	0.248
r_nbd_other	0.245
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.212
r_xyhbond_nbd_refined	0.197
r_chiral_restr	0.103
r_nbtor_other	0.089
r_metal_ion_refined	0.051
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	179
Heterogen Atoms	12

Software

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