2ESC

Crystal structure of a 40 KDa protective signalling protein from Bovine (SPC-40) at 2.1 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LJY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829825mM TRIS-HCL, 50mM NACL, 19% ETHANOL , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.7855.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.683α = 90
b = 67.417β = 90
c = 106.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMIRROR2003-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.12097.80.0778.82779627796
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1897.80.4472

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1LJY2.1202779625190132497.780.175730.173420.22021RANDOM36.152
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]
-0.22-0.120.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg21.373
r_dihedral_angle_1_deg4.874
r_scangle_it4.25
r_scbond_it2.58
r_angle_refined_deg2.042
r_mcangle_it1.982
r_angle_other_deg1.494
r_mcbond_it1.034
r_nbtor_other0.561
r_nbd_refined0.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg21.373
r_dihedral_angle_1_deg4.874
r_scangle_it4.25
r_scbond_it2.58
r_angle_refined_deg2.042
r_mcangle_it1.982
r_angle_other_deg1.494
r_mcbond_it1.034
r_nbtor_other0.561
r_nbd_refined0.238
r_nbd_other0.226
r_symmetry_vdw_refined0.21
r_symmetry_vdw_other0.209
r_chiral_restr0.176
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_other0.1
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2874
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement