4LPI

A sperm whale myoglobin double mutant L29H/F43Y Mb with a distal hydrogen-bonding network


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IT8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate, 30% w/v Polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277KK
Crystal Properties
Matthews coefficientSolvent content
2.1743.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.884α = 90
b = 48.184β = 90
c = 78.458γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9793SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.3635.557.63268021

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT4IT81.3635.550.2332680200098.220.18120.18010.199115.3793
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]
-1.6534-0.34221.9956
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.985
f_angle_d1.132
f_chiral_restr0.072
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1219
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms43

Software

Software
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement