3DMK | pdb_00003dmk

Crystal structure of Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V5M	PDB entry 2V5M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	1.28M Ammonium sulfate, 0.2M MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.24	70.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.46	α = 90
b = 177.61	β = 90
c = 434.05	γ = 90

Symmetry
Space Group	I 2 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		2007-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.97970	ALS	8.2.2

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	4.19	90	99.9	0.066	9	8.7	34106	34106		-3	59.8

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	4.19	4.46	99.9		0.462		8.6	5605

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 2V5M	4.19	12	32525	1618	99.37	0.282	0.28	0.28	0.327	0.33	RANDOM	54.028

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]
0.1			-2.07		1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.378
r_dihedral_angle_3_deg	14.899
r_dihedral_angle_4_deg	13.021
r_dihedral_angle_1_deg	5.55
r_mcangle_it	1.438
r_scangle_it	1.277
r_mcbond_it	1.042
r_angle_refined_deg	1.029
r_angle_other_deg	0.778
r_scbond_it	0.757

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.378
r_dihedral_angle_3_deg	14.899
r_dihedral_angle_4_deg	13.021
r_dihedral_angle_1_deg	5.55
r_mcangle_it	1.438
r_scangle_it	1.277
r_mcbond_it	1.042
r_angle_refined_deg	1.029
r_angle_other_deg	0.778
r_scbond_it	0.757
r_mcbond_other	0.128
r_chiral_restr	0.057
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16431
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	309

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.