5EET

Crystal structure of murine neuroglobin 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
2.5852.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.316α = 90
b = 88.316β = 90
c = 114.457γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMAR CCD 165 mm2012-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE CRISTAL0.4540SOLEILCRISTAL

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
1245.82198.70.1040.1190.05610.241162311623
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)
122.1199.70.4790.4790.2561.54.11685

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 REPLACEMENTTHROUGHOUT4O4T2201105855298.10.14490.14310.1805RANDOM29.779
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]
0.120.060.12-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.755
r_dihedral_angle_4_deg17.697
r_dihedral_angle_3_deg15.933
r_dihedral_angle_1_deg5.049
r_mcangle_it4.192
r_mcbond_it2.773
r_mcbond_other2.773
r_angle_other_deg2.144
r_angle_refined_deg1.879
r_chiral_restr0.131
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.755
r_dihedral_angle_4_deg17.697
r_dihedral_angle_3_deg15.933
r_dihedral_angle_1_deg5.049
r_mcangle_it4.192
r_mcbond_it2.773
r_mcbond_other2.773
r_angle_other_deg2.144
r_angle_refined_deg1.879
r_chiral_restr0.131
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1172
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
DMphasing
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
BUCCANEERphasing