2VME | pdb_00002vme

Structure of the wild-type discoidin II from Dictyostelium discoideum

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		8.5		20% PEG 4K, 10 MM CDCL2, 100 MM HEPES PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 287.885	α = 90
b = 56.281	β = 109.1
c = 123.674	γ = 90

Symmetry
Space Group	C 1 2 1

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		2006-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	2.45	26.82	96.8	0.09	5.8	3.2		66709		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	2.45	2.58	98.3		0.37	1.9	3.1

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 (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	2.45	26.8	63327	3380	95.9	0.184	0.181	0.18	0.238	0.24	RANDOM	26.78

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]
-1.5		-0.74	0.99		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.118
r_dihedral_angle_4_deg	20.218
r_dihedral_angle_3_deg	15.283
r_dihedral_angle_1_deg	7.464
r_scangle_it	2.689
r_scbond_it	1.851
r_angle_refined_deg	1.556
r_mcangle_it	1.185
r_mcbond_it	0.682
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.1
r_symmetry_hbond_refined	0.046
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
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	12084
Nucleic Acid Atoms
Solvent Atoms	543
Heterogen Atoms	113

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing