4AB8

Fragments bound to bovine trypsin for the SAMPL challenge


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K1MPDB ENTRY 1K1M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.822.5% PEG 3350, 0.18 M AMMONIUM SULFATE, 0.12 M SODIUM THIOCYANATE, 0.09 M BIS-TRIS PH 5.5, 0.01 M TRIS PH 8.5 (FINAL MEASURED PH=5.82). THE PROTEIN WAS AT 2 MM (47 MG/ML), WITH 4 MM BENZYLAMINE AND 10 MM CALCIUM CHLORIDE ADDED TO STABILIZE IT. THE CRYSTALLIZATIONS WERE SET UP WITH A PHOENITO PROTOCOL (NEWMAN ET AL. 2008), WHERE A PHOENIX ROBOT (ART ROBBINS INSTRUMENTS, SUNNYSIDE, CA) WAS USED TO DISPENSE THE PROTEIN INTO AN SD2 CRYSTALLIZATION PLATE (PRE-FILLED WITH 50 ML RESERVOIR SOLUTION) AND A MOSQUITO ROBOT (TTP LABTECH, MELBOURN, UK) WAS USED TO DISPENSE THE RESERVOIR SOLUTION AND SEED STOCK OVER THE PROTEIN DROPLET.
Crystal Properties
Matthews coefficientSolvent content
1.9236.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.323α = 90
b = 54.323β = 90
c = 105.32γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2011-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX1Australian SynchrotronMX1

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
11.652.799.90.0722.610244611
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)
11.61.6999.90.663.48.7

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 1K1M1.647.0523176124299.970.170590.168780.2047RANDOM16.709
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]
-0.34-0.17-0.340.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.851
r_dihedral_angle_4_deg17.195
r_dihedral_angle_3_deg14.173
r_dihedral_angle_1_deg6.502
r_angle_refined_deg2.253
r_chiral_restr0.162
r_bond_refined_d0.022
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.851
r_dihedral_angle_4_deg17.195
r_dihedral_angle_3_deg14.173
r_dihedral_angle_1_deg6.502
r_angle_refined_deg2.253
r_chiral_restr0.162
r_bond_refined_d0.022
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms1629
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing