5ILM

H64A sperm whale myoglobin with a Fe-chlorophenyl moiety


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE9293100 mM Tris-HCl pH 9.0, 1 mM EDTA, 2.3 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.1160.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.599α = 90
b = 90.599β = 90
c = 45.121γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200Kmirrors2014-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7501000.0649.29.123456
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)
11.71.731000.4746.2

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 REPLACEMENTTHROUGHOUT2MBW1.74022177111799.270.15390.15190.1921RANDOM17.412
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]
0.050.020.05-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.112
r_sphericity_bonded20.282
r_dihedral_angle_4_deg18.276
r_dihedral_angle_3_deg14.389
r_rigid_bond_restr6.184
r_dihedral_angle_1_deg5.04
r_angle_refined_deg2.418
r_mcangle_it2.085
r_mcbond_it1.481
r_mcbond_other1.467
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.112
r_sphericity_bonded20.282
r_dihedral_angle_4_deg18.276
r_dihedral_angle_3_deg14.389
r_rigid_bond_restr6.184
r_dihedral_angle_1_deg5.04
r_angle_refined_deg2.418
r_mcangle_it2.085
r_mcbond_it1.481
r_mcbond_other1.467
r_angle_other_deg1.14
r_chiral_restr0.134
r_bond_refined_d0.025
r_gen_planes_refined0.015
r_gen_planes_other0.006
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1212
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms87

Software

Software
Software NamePurpose
HKL-3000phasing
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction