3HQ6

Cytochrome c peroxidase from G. sulfurreducens, wild type


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EB7PDB ENTRY 1EB7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429316 % PEG 10000 0.1 M HEPES/NaOH, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5151

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.241α = 68.69
b = 55.783β = 71.84
c = 78.644γ = 57.76
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2007-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X121.05EMBL/DESY, HAMBURGX12

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
127096.40.097.934842822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.197.70.2850.28533

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1EB727024842843589231994.640.193090.189090.26606RANDOM24.014
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]
0.44-2.550.772.8-0.71-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.148
r_dihedral_angle_3_deg18.769
r_dihedral_angle_4_deg15.383
r_dihedral_angle_1_deg7.539
r_scangle_it4.745
r_scbond_it3.419
r_angle_refined_deg2.221
r_mcangle_it2.049
r_mcbond_it1.366
r_symmetry_hbond_refined0.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.148
r_dihedral_angle_3_deg18.769
r_dihedral_angle_4_deg15.383
r_dihedral_angle_1_deg7.539
r_scangle_it4.745
r_scbond_it3.419
r_angle_refined_deg2.221
r_mcangle_it2.049
r_mcbond_it1.366
r_symmetry_hbond_refined0.332
r_nbtor_refined0.31
r_symmetry_vdw_refined0.28
r_nbd_refined0.256
r_xyhbond_nbd_refined0.21
r_chiral_restr0.142
r_metal_ion_refined0.08
r_bond_refined_d0.028
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4821
Nucleic Acid Atoms
Solvent Atoms721
Heterogen Atoms174

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling