6I40

Crystal structure of murine neuroglobin bound to CO at 15K under illumination using optical fiber


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q1F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M NA ACETATE, 2M NA FORMATE, Ph 4.6
Crystal Properties
Matthews coefficientSolvent content
2.4349.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.043α = 90
b = 88.043β = 90
c = 110.16γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray15CCDADSC QUANTUM 42010-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.944.6398.50.05516.93.712847
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9299.90.37333.6

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 SYNTHESISTHROUGHOUT1q1f1.936.041221162897.690.169490.167320.21454RANDOM26.567
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_deg33.095
r_dihedral_angle_3_deg17.357
r_dihedral_angle_4_deg16.505
r_dihedral_angle_1_deg5.096
r_scangle_it2.973
r_scbond_it1.878
r_angle_refined_deg1.373
r_mcangle_it1.309
r_mcbond_it0.765
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.095
r_dihedral_angle_3_deg17.357
r_dihedral_angle_4_deg16.505
r_dihedral_angle_1_deg5.096
r_scangle_it2.973
r_scbond_it1.878
r_angle_refined_deg1.373
r_mcangle_it1.309
r_mcbond_it0.765
r_nbtor_refined0.303
r_xyhbond_nbd_refined0.274
r_nbd_refined0.271
r_symmetry_vdw_refined0.233
r_symmetry_hbond_refined0.18
r_chiral_restr0.104
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
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 Atoms96
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
REFMACphasing