2Y5A

Cytochrome c peroxidase (CCP) W191G bound to 3-aminopyridine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AC4PDB ENTRY 1AC4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1CRYSTAL WAS SOAKED IN: 125 MM ACETIC ACID / BTP PH 4.5, 25% MPD.
Crystal Properties
Matthews coefficientSolvent content
3.160.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.853α = 90
b = 75.362β = 90
c = 106.884γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.253099.20.0342.33.7113329
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)
11.251.2997.50.184.53

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1AC41.2525.18107546567299.20.150260.149520.16388RANDOM16.922
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]
0.21-0.60.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.722
r_dihedral_angle_4_deg25.362
r_dihedral_angle_3_deg11.444
r_dihedral_angle_1_deg5.569
r_scangle_it2.719
r_scbond_it1.82
r_mcangle_it1.33
r_angle_refined_deg1.104
r_mcbond_it0.774
r_rigid_bond_restr0.739
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.722
r_dihedral_angle_4_deg25.362
r_dihedral_angle_3_deg11.444
r_dihedral_angle_1_deg5.569
r_scangle_it2.719
r_scbond_it1.82
r_mcangle_it1.33
r_angle_refined_deg1.104
r_mcbond_it0.774
r_rigid_bond_restr0.739
r_chiral_restr0.083
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2317
Nucleic Acid Atoms
Solvent Atoms440
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing