1LYC

The impact of the physical and chemical enviroment on the molecular structure of Coprinus cinereus peroxidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherfuture PDB deposition

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.252931.5M-1.6M NH4H2PO, pH 4.0-4.5, VAPOR DIFFUSION, HANGING DROP, pH 4.25, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3146.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.289α = 90
b = 115.055β = 90
c = 36.97γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1998-09-23MSINGLE WAVELENGTH
21x-ray100IMAGE PLATERIGAKU RAXIS IIC1999-08-27MSINGLE WAVELENGTH
31x-ray100IMAGE PLATEMARRESEARCH2000-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.8346EMBL/DESY, HAMBURGBW7B
2ROTATING ANODERIGAKU1.5418
3ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
1,2,31.5715990.1390.1394714846580-328.9
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)
1.571.6960.2230.223

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 REPLACEMENTTHROUGHOUTfuture PDB deposition1.5714.898917646580422798.30.2250.2230.2230.265RANDOM34
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]
-10.25-5.5815.83
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22
c_angle_deg1.5
c_mcangle_it1.25
c_improper_angle_d1
c_mcbond_it0.78
c_scangle_it0.67
c_scbond_it0.42
c_bond_d0.019
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22
c_angle_deg1.5
c_mcangle_it1.25
c_improper_angle_d1
c_mcbond_it0.78
c_scangle_it0.67
c_scbond_it0.42
c_bond_d0.019
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4918
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms90

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement