2VMD | pdb_00002vmd

Structure of the complex of discoidin II from Dictyostelium discoideum with beta-methyl-galactose

X-RAY DIFFRACTION

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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 % PEG550 MME, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.14	α = 90
b = 81.14	β = 90
c = 259.28	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		2006-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	36.7	99.7	0.06	8.7	4.4		26194		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	2.01	98.6		0.31	2.35	4.06

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 2VM9	1.9	36.74	24868	1326	99.6	0.181	0.178	0.18	0.227	0.23	RANDOM	25.9

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]
1.58	0.79		1.58		-2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.856
r_dihedral_angle_4_deg	19.319
r_dihedral_angle_3_deg	13.827
r_dihedral_angle_1_deg	7.426
r_scangle_it	3.483
r_scbond_it	2.361
r_angle_refined_deg	1.494
r_mcangle_it	1.465
r_mcbond_it	0.878
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.108
r_bond_refined_d	0.014
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	228
Heterogen Atoms	37

Software

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