2W6W

Crystal structure of recombinant Sperm Whale Myoglobin under 1atm of Xenon


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.52.6M (NH4)2SO4, 0.1M TRIS/HCL, PH8.5
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-ray100IMAGE PLATERIGAKU-MSCOSMIC MIRRORS2000-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
11.9819.6898.10.0573.215044216.2
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)
11.982.0197.30.123.13.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1NAZ1.99201402074199.60.1890.1880.205RANDOM11.53
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]
0.210.110.21-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.442
r_dihedral_angle_4_deg14.4
r_dihedral_angle_3_deg12.328
r_dihedral_angle_1_deg4.151
r_scangle_it1.291
r_angle_refined_deg0.875
r_scbond_it0.743
r_mcangle_it0.431
r_nbtor_refined0.29
r_mcbond_it0.201
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.442
r_dihedral_angle_4_deg14.4
r_dihedral_angle_3_deg12.328
r_dihedral_angle_1_deg4.151
r_scangle_it1.291
r_angle_refined_deg0.875
r_scbond_it0.743
r_mcangle_it0.431
r_nbtor_refined0.29
r_mcbond_it0.201
r_nbd_refined0.174
r_symmetry_vdw_refined0.147
r_xyhbond_nbd_refined0.083
r_symmetry_hbond_refined0.079
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.002
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 Atoms1217
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing