5HMJ

Re-refinement of 4xan: hen lysozyme with carboplatin in sodium bromide solution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XAN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.7297CO-CRYSTALLIZING 20 MG ML HEWL WITH 1.4 MG CARBOPLATIN IN 75 MicroL DMSO, 462.5 MicroL 0.1 M SODIUM ACETATE, 462.5 MicroL 1 M NABR SOLUTION., PH 4.7, BATCH MODE, TEMPERATURE 297K .
Crystal Properties
Matthews coefficientSolvent content
1.9235.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.58α = 90
b = 78.58β = 90
c = 37.29γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9163DiamondI04

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
11.339.2979.090.0954.5910.82308814.8164861805
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)
11.31.34631.052.0580.232.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4xan1.2999010298939.290.40996172399323088218379.09352465580.1666383735270.1642045743950.214997648104Random19.8326076049
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.2929399304
f_angle_d1.18333899677
f_chiral_restr0.0844146767182
f_bond_d0.0100569036924
f_plane_restr0.00544896578564
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms28

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing
EVALdata scaling
EVALdata reduction