2J16

Apo & Sulphate bound forms of SDP-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherENSEMBLE MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP1.5M MGSO4, 0.1M HEPES, PH 7.5 7MG/ML PROTEIN 1:1 SITTING DROP VAPOUR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
3.6566.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.342α = 90
b = 77.342β = 90
c = 152.885γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2000-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.73099.70.064.3133961
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)
12.72.899.80.37

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 REPLACEMENTTHROUGHOUTENSEMBLE MODEL2.719.771258365299.20.2320.230.257RANDOM42.49
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]
0.160.16-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.411
r_dihedral_angle_4_deg18.589
r_dihedral_angle_3_deg16.249
r_dihedral_angle_1_deg5.635
r_scangle_it1.425
r_angle_refined_deg1.196
r_mcangle_it1.037
r_scbond_it0.869
r_mcbond_it0.571
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.411
r_dihedral_angle_4_deg18.589
r_dihedral_angle_3_deg16.249
r_dihedral_angle_1_deg5.635
r_scangle_it1.425
r_angle_refined_deg1.196
r_mcangle_it1.037
r_scbond_it0.869
r_mcbond_it0.571
r_nbtor_refined0.304
r_nbd_refined0.194
r_symmetry_vdw_refined0.162
r_symmetry_hbond_refined0.131
r_xyhbond_nbd_refined0.111
r_chiral_restr0.083
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms2179
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing