2VM9

Native structure of the recombinant discoidin II of Dictyostelium discoideum at 1.75 angstrom


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherMERCURY STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5200 MM AMMONIUM PHOSPHATE MONOBASIC, 100 MM TRIS PH 8.5, 50 % MPD
Crystal Properties
Matthews coefficientSolvent content
2.9157.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.833α = 90
b = 81.833β = 90
c = 257.823γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.75371000.087.510.9340432
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.841000.352.111

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTMERCURY STRUCTURE1.75403230917251000.1510.150.178RANDOM12.21
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]
0.120.060.12-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.07
r_dihedral_angle_4_deg16.014
r_dihedral_angle_3_deg12.345
r_dihedral_angle_1_deg6.956
r_scangle_it3.184
r_scbond_it2.089
r_angle_refined_deg1.492
r_mcangle_it1.329
r_mcbond_it0.814
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.07
r_dihedral_angle_4_deg16.014
r_dihedral_angle_3_deg12.345
r_dihedral_angle_1_deg6.956
r_scangle_it3.184
r_scbond_it2.089
r_angle_refined_deg1.492
r_mcangle_it1.329
r_mcbond_it0.814
r_nbtor_refined0.309
r_symmetry_vdw_refined0.215
r_nbd_refined0.208
r_symmetry_hbond_refined0.203
r_xyhbond_nbd_refined0.131
r_chiral_restr0.107
r_bond_refined_d0.014
r_gen_planes_refined0.006
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 AtomsNumber
Protein Atoms1986
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing