6E03 | pdb_00006e03

sperm whale myoglobin nitrosoethane adduct


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2982.56-3.20 M AS, 100 mM Tris-HCl, 1 mm EDTA, pH 7.4 or 9.0.
Crystal Properties
Matthews coefficientSolvent content
3.0759.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.272α = 90
b = 90.272β = 90
c = 45.316γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2017-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7645.1496.4216.23720356
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.79

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.7645.141941196096.240.161340.159920.170.190810.21RANDOM13.689
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]
0.110.060.11-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.359
r_dihedral_angle_4_deg19.928
r_dihedral_angle_3_deg14.653
r_long_range_B_other5.513
r_long_range_B_refined5.511
r_dihedral_angle_1_deg5.307
r_scangle_other4.169
r_scbond_it2.842
r_scbond_other2.84
r_angle_refined_deg1.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.359
r_dihedral_angle_4_deg19.928
r_dihedral_angle_3_deg14.653
r_long_range_B_other5.513
r_long_range_B_refined5.511
r_dihedral_angle_1_deg5.307
r_scangle_other4.169
r_scbond_it2.842
r_scbond_other2.84
r_angle_refined_deg1.789
r_mcangle_it1.6
r_mcangle_other1.6
r_angle_other_deg1.157
r_mcbond_it1.142
r_mcbond_other1.132
r_chiral_restr0.086
r_bond_refined_d0.016
r_gen_planes_refined0.011
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 Atoms1217
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms73

Software

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