X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FK7pdb entry 4fk7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.22915 micromoles of suramin and 1:100 mol/mol of elastase were added to protein stock solution. Crystallization condition: 2.4M sodium malonate, 0.01M HEPES, pH 7.2, vapor diffusion, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.855.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.725α = 90
b = 95.966β = 90
c = 190.839γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97625CLSI08ID-1

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
12.20695.4298.90.09312.87.35396153961
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3798.30.9240.9240.87.77774

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 REPLACEMENTTHROUGHOUTpdb entry 4fk72.254053925148698.4480.2220.22110.2511THIN SHELLS (SFTOOLS)56.268
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]
-1.8414.524-2.683
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.423
r_dihedral_angle_4_deg18.766
r_dihedral_angle_3_deg15.25
r_dihedral_angle_1_deg5.832
r_angle_refined_deg1.27
r_angle_other_deg0.982
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.423
r_dihedral_angle_4_deg18.766
r_dihedral_angle_3_deg15.25
r_dihedral_angle_1_deg5.832
r_angle_refined_deg1.27
r_angle_other_deg0.982
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6734
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms6

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction