3TXF

HEWL co-crystallization with cisplatin in DMSO media with glycerol 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 glycerol as cryoprotectant, pH 4.7, BATCH, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9838.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.443α = 90
b = 78.443β = 90
c = 36.971γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Incoatec Helios confocal optics2011-02-17MSINGLE 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
11.6955.4792.60.0370.03720.813.1113407121484220.8
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)
11.691.7975.20.1557.825.9613704

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 2W1Y1.6955.4724134071214862395.260.20880.178580.175230.24857RANDOM23.617
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
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.365
r_dihedral_angle_4_deg14.948
r_dihedral_angle_3_deg13.023
r_dihedral_angle_1_deg6.774
r_scangle_it4.63
r_scbond_it3.162
r_angle_refined_deg2.071
r_mcangle_it1.877
r_mcbond_it1.278
r_chiral_restr0.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.365
r_dihedral_angle_4_deg14.948
r_dihedral_angle_3_deg13.023
r_dihedral_angle_1_deg6.774
r_scangle_it4.63
r_scbond_it3.162
r_angle_refined_deg2.071
r_mcangle_it1.877
r_mcbond_it1.278
r_chiral_restr0.171
r_bond_refined_d0.022
r_gen_planes_refined0.011
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 Atoms107
Heterogen Atoms201

Software

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