3TXG

HEWL co-crystallization with cisplatin in DMSO media with paratone as the cryoprotectant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH4.729549 mg HEWL + 3 mg cisplatin in 462.5 uL 0.04 M sodium acetate + 75 uL DMSO + 462.5 uL 10% sodium chloride, with paratone as cryoprotectant, pH 4.7, BATCH, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9737.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.081α = 90
b = 78.081β = 90
c = 37.107γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Incoatec Helios confocal optics2010-11-25MSINGLE 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)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
11.737.193.80.0230.02325.6624.2713147123424214.7
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)
11.71.897.10.1734.0216.2113147

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2W1Y1.734.9224131471234264199.130.18520.184370.181560.23922RANDOM17.939
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.663
r_dihedral_angle_4_deg18.804
r_dihedral_angle_3_deg12.464
r_dihedral_angle_1_deg6.155
r_scangle_it5.523
r_scbond_it3.668
r_angle_refined_deg1.911
r_mcangle_it1.9
r_mcbond_it1.178
r_chiral_restr0.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.663
r_dihedral_angle_4_deg18.804
r_dihedral_angle_3_deg12.464
r_dihedral_angle_1_deg6.155
r_scangle_it5.523
r_scbond_it3.668
r_angle_refined_deg1.911
r_mcangle_it1.9
r_mcbond_it1.178
r_chiral_restr0.156
r_bond_refined_d0.021
r_gen_planes_refined0.01
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_other
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 Atoms98
Heterogen Atoms80

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling