1ZBY

High-Resolution Crystal Structure of Native (Resting) Cytochrome c Peroxidase (CcP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CYPPDB Entry 2CYP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP627730% 2-methyl-2,4-pentanediol (MPD), 50mM Tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6753.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.673α = 90
b = 75.513β = 90
c = 50.994γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCHMirrors1999-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.78SSRLBL9-1

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
11.210096.80.07112.210.05127519312677522
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)
1.21.22740.4371.99

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 2CYP1.2100124130120831311696.20.11620.11320.11320.1495RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
1822223123
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.118
s_non_zero_chiral_vol0.093
s_zero_chiral_vol0.082
s_anti_bump_dis_restr0.063
s_similar_adp_cmpnt0.048
s_angle_d0.029
s_from_restr_planes0.0279
s_bond_d0.015
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2409
Nucleic Acid Atoms
Solvent Atoms837
Heterogen Atoms43

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
DPSdata reduction
MOSFLMdata reduction
SHELXphasing