2RBV

Cytochrome C Peroxidase in complex with (1-methyl-1h-pyrrol-2-yl)-methylamine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16291MES, MPD, pH 6.0, vapor diffusion, hanging drop, temperature 291K, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
3.1160.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.011α = 90
b = 75.699β = 90
c = 107.062γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315KOHZU: DOUBLE CRYSTAL SI(111)2007-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.395099.10.04519.23.982773
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)
11.391.4493.90.2023.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1AC41.393082707827074146990.1390.1380.154RANDOM10.85
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]
0.250.54-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.041
r_dihedral_angle_4_deg24.407
r_dihedral_angle_3_deg11.319
r_dihedral_angle_1_deg5.489
r_sphericity_free4.327
r_sphericity_bonded2.44
r_scangle_it2.206
r_scbond_it1.7
r_rigid_bond_restr1.225
r_angle_refined_deg1.191
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.041
r_dihedral_angle_4_deg24.407
r_dihedral_angle_3_deg11.319
r_dihedral_angle_1_deg5.489
r_sphericity_free4.327
r_sphericity_bonded2.44
r_scangle_it2.206
r_scbond_it1.7
r_rigid_bond_restr1.225
r_angle_refined_deg1.191
r_mcangle_it1.15
r_mcbond_it0.958
r_angle_other_deg0.884
r_mcbond_other0.386
r_nbd_refined0.22
r_symmetry_vdw_other0.22
r_symmetry_hbond_refined0.216
r_nbd_other0.187
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.109
r_symmetry_vdw_refined0.103
r_nbtor_other0.084
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2341
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms56

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing