2W6Y

Crystal structure of Sperm Whale Myoglobin mutant YQR in complex with Xenon


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NAZPDB ENTRY 1NAZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.72.6M (NH4)2SO4, 0.1M TRIS/HCL, PH8.5, pH 8.7
Crystal Properties
Matthews coefficientSolvent content
2.455

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.626α = 90
b = 90.626β = 90
c = 45.505γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2000-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2RELETTRA5.2R

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
11.626.11000.0615.25.728029212.2
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)
11.61.999.90.173.25.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NAZ1.62622658414081000.1650.196RANDOM10.55
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]
0.030.020.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.579
r_dihedral_angle_4_deg17.711
r_dihedral_angle_3_deg13.312
r_dihedral_angle_1_deg4.249
r_scangle_it3.154
r_scbond_it2.179
r_mcangle_it1.382
r_angle_refined_deg1.188
r_mcbond_it0.856
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.579
r_dihedral_angle_4_deg17.711
r_dihedral_angle_3_deg13.312
r_dihedral_angle_1_deg4.249
r_scangle_it3.154
r_scbond_it2.179
r_mcangle_it1.382
r_angle_refined_deg1.188
r_mcbond_it0.856
r_nbtor_refined0.314
r_nbd_refined0.22
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.118
r_symmetry_hbond_refined0.098
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms1224
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing