5IKS

Wild-type sperm whale myoglobin with a Fe-phenyl moiety


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2MBW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42930.1 M Tris-HCl, pH 7.4, 1mM EDTA, 2.5 M Ammonium Sulfate
Crystal Properties
Matthews coefficientSolvent content
1.935.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.484α = 90
b = 30.152β = 105.16
c = 64.463γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200Kmirrors2014-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
11.875097.10.03218.73.610468
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)
11.871.992.20.3093

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2MBW1.8733.28998747696.290.21560.21290.2781RANDOM20.191
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]
0.34-0.1-0.580.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.283
r_dihedral_angle_4_deg32.78
r_dihedral_angle_3_deg15.271
r_dihedral_angle_1_deg5.302
r_angle_refined_deg1.631
r_mcangle_it1.278
r_angle_other_deg1.004
r_mcbond_it0.748
r_mcbond_other0.74
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.283
r_dihedral_angle_4_deg32.78
r_dihedral_angle_3_deg15.271
r_dihedral_angle_1_deg5.302
r_angle_refined_deg1.631
r_mcangle_it1.278
r_angle_other_deg1.004
r_mcbond_it0.748
r_mcbond_other0.74
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1203
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms60

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000phasing
HKL-3000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction