5F0B

Crystal structure of murine neuroglobin mutant F106W at 280 MPa 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
2.4549.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.212α = 90
b = 86.212β = 90
c = 114.459γ = 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
12.14645.4211000.1510.1610.05410.28.89151915130.74
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)
12.1462.271000.8630.8630.3060.88.91318

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 REPLACEMENTTHROUGHOUT4O4T2.14620843842496.650.17410.17060.238RANDOM41.111
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]
-0.06-0.03-0.060.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.943
r_dihedral_angle_3_deg19.983
r_dihedral_angle_4_deg15.649
r_mcangle_it7.422
r_dihedral_angle_1_deg6.454
r_mcbond_it5.285
r_mcbond_other5.197
r_angle_refined_deg2.451
r_angle_other_deg2.031
r_chiral_restr0.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.943
r_dihedral_angle_3_deg19.983
r_dihedral_angle_4_deg15.649
r_mcangle_it7.422
r_dihedral_angle_1_deg6.454
r_mcbond_it5.285
r_mcbond_other5.197
r_angle_refined_deg2.451
r_angle_other_deg2.031
r_chiral_restr0.174
r_bond_refined_d0.027
r_gen_planes_refined0.014
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 Atoms73
Heterogen Atoms48

Software

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