5EQM

Crystal structure of murine neuroglobin at 310 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
2.550.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.372α = 90
b = 87.372β = 90
c = 113.284γ = 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
12.0545.34597.60.1120.1260.0579.851034010340
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)
12.052.1697.80.5410.5410.2681.351509

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 REPLACEMENTTHROUGHOUT4O4T2.0520946347793.130.17460.17160.2371RANDOM33.088
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]
-0.04-0.02-0.040.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.825
r_dihedral_angle_4_deg21.628
r_dihedral_angle_3_deg15.984
r_dihedral_angle_1_deg6.713
r_mcangle_it5.709
r_mcbond_it3.93
r_mcbond_other3.92
r_angle_refined_deg2.219
r_angle_other_deg2.014
r_chiral_restr0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.825
r_dihedral_angle_4_deg21.628
r_dihedral_angle_3_deg15.984
r_dihedral_angle_1_deg6.713
r_mcangle_it5.709
r_mcbond_it3.93
r_mcbond_other3.92
r_angle_refined_deg2.219
r_angle_other_deg2.014
r_chiral_restr0.17
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_gen_planes_other0.005
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1172
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms48

Software

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