5HLU

X-ray crystal structure of met F43H/H64A sperm whale myoglobin in complex with nitric oxide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OF9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29330%(w/v) Polyethylene glycol 8,000, 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.2444.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.69α = 90
b = 49.528β = 90
c = 77.598γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDRIGAKU2016-01-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.988SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.55099.80.0730.07314.63.423916
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5399.80.0730.073216.4

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 REPLACEMENTTHROUGHOUT4OF91.541.7523916128499.840.141910.140970.1594RANDOM11.296
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]
-0.320.010.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.457
r_dihedral_angle_4_deg17.732
r_dihedral_angle_3_deg11.3
r_long_range_B_refined6.551
r_long_range_B_other5.641
r_dihedral_angle_1_deg4.696
r_scangle_other4.329
r_scbond_other2.869
r_scbond_it2.867
r_angle_refined_deg2.356
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.457
r_dihedral_angle_4_deg17.732
r_dihedral_angle_3_deg11.3
r_long_range_B_refined6.551
r_long_range_B_other5.641
r_dihedral_angle_1_deg4.696
r_scangle_other4.329
r_scbond_other2.869
r_scbond_it2.867
r_angle_refined_deg2.356
r_mcangle_other1.418
r_mcangle_it1.402
r_mcbond_it1.018
r_angle_other_deg0.974
r_mcbond_other0.953
r_chiral_restr0.162
r_bond_refined_d0.027
r_gen_planes_refined0.015
r_gen_planes_other0.008
r_bond_other_d0.001
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 Atoms1203
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
MOLREPphasing
HKL-3000data reduction