4LT3

HEWL co-crystallized with Carboplatin in non-NaCl conditions: crystal 2 processed using the XDS software package


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W1YPDB ENTRY 2W1Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42942 uL protein/carboplatin/DMSO solution [20 mg (0.6 mM) HEWL + 1.4 mg (1.8 mM) carboplatin in 1 mL distilled water + 75 uL DMSO] + 2 uL reservoir solution [65% MPD, 0.1 M citric acid, pH 4.0] against 1 mL of reservoir solution, crystals grew after ~4 weeks, data collected 5 weeks after crystal growth, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
1.935.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.12α = 90
b = 77.12β = 90
c = 36.56γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray127CCDAPEX II CCD2013-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
1239.41950.24814.67850748840.5
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)
122.0532.42.270.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB ENTRY 2W1Y227.2847850748836299.610.198650.195740.2575RANDOM27.677
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]
-0.49-0.490.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.357
r_dihedral_angle_4_deg18.895
r_dihedral_angle_3_deg14.729
r_long_range_B_other6.884
r_long_range_B_refined6.882
r_dihedral_angle_1_deg6.592
r_scangle_other4.374
r_scbond_it3.109
r_scbond_other2.827
r_mcangle_other2.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.357
r_dihedral_angle_4_deg18.895
r_dihedral_angle_3_deg14.729
r_long_range_B_other6.884
r_long_range_B_refined6.882
r_dihedral_angle_1_deg6.592
r_scangle_other4.374
r_scbond_it3.109
r_scbond_other2.827
r_mcangle_other2.81
r_mcangle_it2.808
r_mcbond_it1.847
r_mcbond_other1.822
r_angle_refined_deg1.65
r_angle_other_deg0.933
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms41

Software

Software
Software NamePurpose
APEXdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling