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The impact of the physical and chemical enviroment on the molecular structure of Coprinus cinereus peroxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other future PDB deposition
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.25 293 1.5M-1.6M NH4H2PO, pH 4.0-4.5, VAPOR DIFFUSION, HANGING DROP, pH 4.25, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.289 α = 90 b = 115.055 β = 90 c = 36.97 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 1998-09-23 M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IIC 1999-08-27 M SINGLE WAVELENGTH 3 1 x-ray 100 IMAGE PLATE MARRESEARCH 2000-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8346 EMBL/DESY, HAMBURG BW7B 2 ROTATING ANODE RIGAKU 1.5418 3 ROTATING ANODE RIGAKU 1.5418
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1,2,3 1.57 15 99 0.139 0.139 47148 46580 -3 28.9
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) Redundancy Number Unique Reflections (All) 1.57 1.6 96 0.223 0.223
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT future PDB deposition 1.57 14.89 89176 46580 4227 98.3 0.225 0.223 0.223 0.2149 0.265 0.2547 RANDOM 34
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 -5.58 15.83
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_angle_deg 1.5 c_mcangle_it 1.25 c_improper_angle_d 1 c_mcbond_it 0.78 c_scangle_it 0.67 c_scbond_it 0.42 c_bond_d 0.019 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_angle_deg 1.5 c_mcangle_it 1.25 c_improper_angle_d 1 c_mcbond_it 0.78 c_scangle_it 0.67 c_scbond_it 0.42 c_bond_d 0.019 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 Atoms Number Protein Atoms 4918 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 90
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement