3F04 | pdb_00003f04

Crystal Structure of Synaptotagmin I C2A domain

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.99	α = 90
b = 38.67	β = 97.26
c = 44.33	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		2005-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979	APS	19-BM

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	1.35	50	97.4	0.047	35.117	6.4		30486

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)
	1.35	1.4	86.2		0.154		5	2688

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.35	28.5	30467	1539	97.29	0.196	0.194	0.19	0.224	0.22	RANDOM	19.814

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	32.108
r_dihedral_angle_4_deg	12.118
r_dihedral_angle_3_deg	8.625
r_dihedral_angle_1_deg	3.927
r_sphericity_bonded	1.994
r_mcangle_it	1.717
r_sphericity_free	1.595
r_scangle_it	1.589
r_angle_refined_deg	1.179
r_mcbond_it	1.135
r_scbond_it	1.09
r_rigid_bond_restr	0.929
r_nbtor_refined	0.319
r_nbd_refined	0.277
r_symmetry_vdw_refined	0.245
r_xyhbond_nbd_refined	0.197
r_symmetry_hbond_refined	0.16
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1112
Nucleic Acid Atoms
Solvent Atoms	356
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling