6EYE

Crystal structure of murine neuroglobin under 150 bar krypton


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52911.6M AMMONIUM SULPHATE, 0.1M MES
Crystal Properties
Matthews coefficientSolvent content
2.5852.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.854α = 90
b = 87.854β = 90
c = 113.21γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.8556ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.745.4199.80.0430.0450.0130.99928.319.61873024
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.899.10.2750.3180.1510.8934.7

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4O4T1.745.411785986699.810.19620.193730.25394RANDOM40.372
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.592
r_dihedral_angle_4_deg20.945
r_dihedral_angle_3_deg16.139
r_long_range_B_refined9.283
r_long_range_B_other9.255
r_scangle_other7.049
r_dihedral_angle_1_deg5.659
r_mcangle_it5.279
r_mcangle_other5.276
r_scbond_it4.656
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.592
r_dihedral_angle_4_deg20.945
r_dihedral_angle_3_deg16.139
r_long_range_B_refined9.283
r_long_range_B_other9.255
r_scangle_other7.049
r_dihedral_angle_1_deg5.659
r_mcangle_it5.279
r_mcangle_other5.276
r_scbond_it4.656
r_scbond_other4.649
r_mcbond_other3.919
r_mcbond_it3.916
r_angle_refined_deg2.241
r_angle_other_deg1.195
r_chiral_restr0.147
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_gen_planes_other0.004
r_bond_other_d0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1172
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing