3O7N

The V59W mutation blocks the distal pocket of the hemoglobin - dehaloperoxidase from Amphitrite ornata


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QFKPDB entry 2QFK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.92770.2 M Ammonium sulfate, 32% w/v PEG 4000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1643.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.925α = 90
b = 67.305β = 90
c = 69.253γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM0.91339APS22-BM

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
11.7237.08940.1679.54.32791326238212
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)
11.721.76597.990.6162.44.32034

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUTPDB entry 2QFK1.7237.0822791326238144694.080.176620.173330.23688RANDOM7.963
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]
0.26-0.330.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.846
r_dihedral_angle_4_deg19.498
r_dihedral_angle_3_deg18.345
r_dihedral_angle_1_deg5.74
r_scangle_it3.723
r_scbond_it2.661
r_angle_refined_deg1.984
r_mcangle_it1.532
r_mcbond_it1.015
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.846
r_dihedral_angle_4_deg19.498
r_dihedral_angle_3_deg18.345
r_dihedral_angle_1_deg5.74
r_scangle_it3.723
r_scbond_it2.661
r_angle_refined_deg1.984
r_mcangle_it1.532
r_mcbond_it1.015
r_chiral_restr0.133
r_bond_refined_d0.023
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2196
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms117

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling