5ILR

H64Q 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
1VAPOR DIFFUSION, HANGING DROP7.4293100 mM Tris-HCl pH 7.4, 1 mM EDTA, 3.0 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
1.935.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.361α = 90
b = 30.315β = 105.21
c = 64.368γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200Kmirrors2014-03-24MSINGLE 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)Rrim I (All)Rpim I (All)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
11.875099.10.0460.0530.02711.63.710786
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)
11.871.998.20.2163

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 REPLACEMENTTHROUGHOUT2MBW1.8733.161025551998.920.1660.16370.2146RANDOM20.368
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]
-0.04-0.650.09-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.494
r_dihedral_angle_4_deg31.449
r_dihedral_angle_3_deg15.712
r_sphericity_bonded6.895
r_dihedral_angle_1_deg5.277
r_mcangle_it2.478
r_angle_refined_deg2.03
r_mcbond_it1.807
r_mcbond_other1.736
r_angle_other_deg1.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.494
r_dihedral_angle_4_deg31.449
r_dihedral_angle_3_deg15.712
r_sphericity_bonded6.895
r_dihedral_angle_1_deg5.277
r_mcangle_it2.478
r_angle_refined_deg2.03
r_mcbond_it1.807
r_mcbond_other1.736
r_angle_other_deg1.107
r_chiral_restr0.129
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_gen_planes_other0.005
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1202
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms71

Software

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