3EK7 | pdb_00003ek7

Calcium-saturated GCaMP2 dimer

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EMA	PDB entries 1EMA and 1CDL
experimental model	PDB	1CDL	PDB entries 1EMA and 1CDL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.2 M lithium sulfate monohydrate, 0.1 M Tris-HCl pH 8.5, 30%(w/v) polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.131	α = 90
b = 47.31	β = 100.48
c = 68.94	γ = 90

Symmetry
Space Group	C 1 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	CCD	MAR CCD 165 mm		2008-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.85	67.73	98.49	0.076		7.5		36788

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	97.6		0.42	5.1	7.6

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 entries 1EMA and 1CDL	1.85	20.67	32223	1714	98.49	0.19129	0.18871	0.2	0.24052	0.25	RANDOM	20.837

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]
-0.09		-0.57	0.6		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.391
r_dihedral_angle_4_deg	17.07
r_dihedral_angle_3_deg	15.393
r_dihedral_angle_1_deg	6.199
r_scangle_it	4.699
r_scbond_it	3.2
r_mcangle_it	1.991
r_angle_refined_deg	1.735
r_mcbond_it	1.404
r_angle_other_deg	0.986
r_symmetry_hbond_refined	0.527
r_mcbond_other	0.316
r_symmetry_vdw_other	0.274
r_nbd_refined	0.218
r_nbd_other	0.199
r_nbtor_refined	0.178
r_metal_ion_refined	0.154
r_xyhbond_nbd_refined	0.15
r_symmetry_vdw_refined	0.148
r_nbtor_other	0.111
r_chiral_restr	0.097
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3105
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	4

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling