1W15 | pdb_00001w15

rat synaptotagmin 4 C2B domain in the presence of calcium

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	7.5		THE RAT SYNAPTOTAGMIN IV C2B DOMAIN WAS CRYSTALLIZED BY THE VAPOR DIFFUSION METHOD (HANGING DROP) BY MIXING 1 MICROLITER PROTEIN (IN 20 MM MES, 150 MM NACL AND 1 MM EDTA, PH 6.32) WITH 1 MICROLITER RESERVOIR SOLUTION (2.5M NACL, 0.1M CACL2, 0.1M HEPES, PH 7.5) SUSPENDED OVER 500 MICROLITERS RESERVOIR SOLUTION. HEXAGONAL CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF 0.1 X 0.1 X 0.2 MM WITHIN TWO DAYS. PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO CRYSTALLIZATION SOLUTION CONTAINING 20% (V/V) ETHYLENE GLYCOL FOR CRYSTALS GROWN IN 0.1 M CACL2, AND THEN COOLED IN LIQUID PROPANE.

Crystal Properties
Matthews coefficient	Solvent content
4.4	72.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.49	α = 90
b = 91.49	β = 90
c = 122.142	γ = 120

Symmetry
Space Group	P 63 2 2

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	CUSTOM		2003-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		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	1.93	37.684	99.9	0.054	41.5	11.9		23368		-3

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	1.93	1.96	99.9		0.719	2.3	8.5

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1K5W	1.93	30	21854	1475	99.9	0.206	0.204	0.21	0.233	RANDOM	42.85

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]
0.26	0.13		0.26		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.182
r_dihedral_angle_3_deg	15.78
r_dihedral_angle_4_deg	12.574
r_dihedral_angle_1_deg	6.377
r_scangle_it	5.166
r_scbond_it	3.159
r_mcangle_it	2.218
r_angle_refined_deg	1.821
r_mcbond_it	1.214
r_nbtor_refined	0.332
r_nbd_refined	0.26
r_symmetry_vdw_refined	0.215
r_symmetry_hbond_refined	0.209
r_xyhbond_nbd_refined	0.2
r_metal_ion_refined	0.152
r_chiral_restr	0.151
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1046
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling