3JZY | pdb_00003jzy

Crystal structure of human Intersectin 2 C2 domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EP6	pdb entry 2EP6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	20% PEG3350, 0.2M calcium chloride. calcium chloride was also added to the protein stock solution to a final concentration of 0.002M. Crystals were detected only after more than 100 days of incubation., vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.125	α = 90
b = 54.125	β = 90
c = 196.709	γ = 90

Symmetry
Space Group	I 41 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	ADSC QUANTUM 315		2009-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97711	APS	19-ID

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	1.56	40	99.9	0.079	13.4	17.7		21447

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)
	1.56	1.59	100		0.89		15.5	1037

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 entry 2EP6	1.56	30	21410	1082	99.86	0.223	0.222	0.2192	0.235	0.2342	RANDOM	19.861

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]
0.142			0.142		-0.284

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.687
r_dihedral_angle_4_deg	14.236
r_dihedral_angle_3_deg	13.21
r_dihedral_angle_1_deg	6.306
r_scangle_it	3.85
r_scbond_it	2.454
r_angle_refined_deg	1.607
r_mcangle_it	1.512
r_mcbond_it	0.848
r_chiral_restr	0.112
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	991
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
Coot	model building
MolProbity	model building