8FDJ

Wild-Type Sperm Whale Myoglobin in Complex with Nitrosobenzene


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2MBWPDB entry 2MBW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42982.56 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA
Crystal Properties
Matthews coefficientSolvent content
1.8734.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.529α = 90
b = 30.049β = 104.55
c = 64.622γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2014-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.755099.70.0360.929.13.113162
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.780.3470.9

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 2MBW1.7533.441236559098.110.230980.228750.27612RANDOM21.128
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]
-0.20.050.160.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.369
r_dihedral_angle_4_deg17.871
r_dihedral_angle_3_deg14.649
r_dihedral_angle_1_deg5.938
r_long_range_B_refined4.442
r_long_range_B_other4.437
r_scangle_other3.587
r_mcangle_it2.389
r_mcangle_other2.388
r_scbond_other2.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.369
r_dihedral_angle_4_deg17.871
r_dihedral_angle_3_deg14.649
r_dihedral_angle_1_deg5.938
r_long_range_B_refined4.442
r_long_range_B_other4.437
r_scangle_other3.587
r_mcangle_it2.389
r_mcangle_other2.388
r_scbond_other2.311
r_scbond_it2.308
r_mcbond_it1.702
r_mcbond_other1.674
r_angle_refined_deg1.578
r_angle_other_deg1.019
r_chiral_restr0.081
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.007
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 Atoms29
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing