3U3E

Complex of Wild Type Myoglobin with Phenol in its Proximal Cavity


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929820mM Tris pH 9.0, 1mM EDTA, 2.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0960.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.309α = 90
b = 90.309β = 90
c = 45.204γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
11.215099.10.06713.36.86434864348
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)
11.211.2393.70.4839.12.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.2131.9476439360493322598.980.145130.143770.17041RANDOM18.3
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]
0.050.030.05-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.534
r_dihedral_angle_4_deg26.02
r_dihedral_angle_3_deg13.01
r_scangle_it7.881
r_scbond_it5.77
r_dihedral_angle_1_deg5.11
r_mcangle_it3.584
r_rigid_bond_restr3.19
r_mcbond_it2.458
r_angle_refined_deg2.408
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.534
r_dihedral_angle_4_deg26.02
r_dihedral_angle_3_deg13.01
r_scangle_it7.881
r_scbond_it5.77
r_dihedral_angle_1_deg5.11
r_mcangle_it3.584
r_rigid_bond_restr3.19
r_mcbond_it2.458
r_angle_refined_deg2.408
r_chiral_restr0.191
r_bond_refined_d0.031
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1214
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing