2VMC

Structure of the complex of discoidin II from Dictyostelium discoideum with N-acetyl-galactosamine

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VM9	PDB ENTRY 2VM9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		25% PEG5550MME, 100 MM HEPES PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.52	α = 90
b = 82.52	β = 90
c = 261.6	γ = 120

Symmetry
Space Group	H 3 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 CCD		2006-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	1.9	48.2	100	0.1	6.5	6		27554		2

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	1.9	2	100		0.34	2.1	6.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2VM9	1.9	43.6	26162	1392	100	0.159	0.157	0.198	RANDOM	16.44

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]
0.37	0.19		0.37		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.198
r_dihedral_angle_4_deg	17.647
r_dihedral_angle_3_deg	12.278
r_dihedral_angle_1_deg	7.196
r_scangle_it	2.945
r_scbond_it	2.018
r_angle_refined_deg	1.412
r_mcangle_it	1.316
r_mcbond_it	0.79
r_nbtor_refined	0.297
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.142
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
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_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	1986
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
AMoRE	phasing