2EUU

Cytochrome c peroxidase (CCP) in complex with 1H-imidazol-2-ylmethanol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AEEPDB Entry: 1AEE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629850 mM KPi 20% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5151

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.675α = 90
b = 73.521β = 90
c = 104.674γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

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
11.455098.50.0599.44.55978759787
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)
1.451.587.90.4564.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry: 1AEE1.45505660056600300598.420.146080.146080.145280.16078RANDOM13.795
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]
1.78-0.72-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.748
r_sphericity_free3.273
r_scangle_it3.25
r_scbond_it2.181
r_sphericity_bonded1.706
r_mcangle_it1.486
r_angle_refined_deg1.328
r_rigid_bond_restr1.163
r_mcbond_it0.901
r_angle_other_deg0.832
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.748
r_sphericity_free3.273
r_scangle_it3.25
r_scbond_it2.181
r_sphericity_bonded1.706
r_mcangle_it1.486
r_angle_refined_deg1.328
r_rigid_bond_restr1.163
r_mcbond_it0.901
r_angle_other_deg0.832
r_symmetry_vdw_other0.332
r_nbd_other0.241
r_nbd_refined0.223
r_xyhbond_nbd_refined0.107
r_symmetry_hbond_refined0.105
r_symmetry_vdw_refined0.093
r_chiral_restr0.088
r_nbtor_other0.085
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2340
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CCP4data scaling
AMoREphasing