3E9U | pdb_00003e9u

Crystal structure of Calx CBD2 domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	8		0.2 M potassium formate, 10 mM CaCl2, 20% Polyethylene glycol 3350, pH 8.0, EVAPORATION

Crystal Properties
Matthews coefficient	Solvent content
4.2	70.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.365	α = 90
b = 113.365	β = 90
c = 41.616	γ = 120

Symmetry
Space Group	P 61

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	NOIR-1		2008-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.000	ALS	4.2.2

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	2.5	38.32	99.8	0.098	18.9	5.1		10260

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.55	99.9		2.5	5.1

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	2.5	38.2	10260	540	100	0.25798	0.25703	0.25	0.27548	0.27	RANDOM	48.735

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]
-1.08	-0.54		-1.08		1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.272
r_dihedral_angle_3_deg	21.296
r_dihedral_angle_4_deg	19.087
r_dihedral_angle_1_deg	8.75
r_angle_refined_deg	1.761
r_scangle_it	1.261
r_scbond_it	0.721
r_mcangle_it	0.72
r_mcbond_it	0.409
r_nbtor_refined	0.313
r_nbd_refined	0.231
r_symmetry_vdw_refined	0.19
r_symmetry_hbond_refined	0.166
r_chiral_restr	0.165
r_xyhbond_nbd_refined	0.143
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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_refined
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1292
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling