5EYS

Crystal structure of murine neuroglobin mutant F106W at ambient pressure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O4T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.6 M ammonium sulfate, 0.1 M MES, 10 % dioxane
Crystal Properties
Matthews coefficientSolvent content
2.652.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.784α = 90
b = 88.784β = 90
c = 114.31γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR555 FLAT PANELmirrors2013-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID090.4104ESRFID09

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.7545.8799.80.0780.0890.04110.84.5176811768123.12
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8499.80.6880.6880.3614.62551

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 REPLACEMENTTHROUGHOUT4O4T1.75201601086295.180.15540.15380.1865RANDOM30.466
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]
0.050.020.05-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.694
r_dihedral_angle_4_deg21.716
r_dihedral_angle_3_deg14.202
r_dihedral_angle_1_deg4.691
r_mcangle_it4.133
r_mcbond_it2.7
r_mcbond_other2.648
r_angle_other_deg2.073
r_angle_refined_deg1.685
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.694
r_dihedral_angle_4_deg21.716
r_dihedral_angle_3_deg14.202
r_dihedral_angle_1_deg4.691
r_mcangle_it4.133
r_mcbond_it2.7
r_mcbond_other2.648
r_angle_other_deg2.073
r_angle_refined_deg1.685
r_chiral_restr0.116
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1175
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms48

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction