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Cytochrome c peroxidase (CCP) in complex with 1H-imidazol-2-ylmethanol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AEE PDB Entry: 1AEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 50 mM KPi
20% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.675 α = 90 b = 73.521 β = 90 c = 104.674 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2005-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.45 50 98.5 0.059 9.4 4.5 59787 59787
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.45 1.5 87.9 0.456 4.1
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 PDB Entry: 1AEE 1.45 50 56600 56600 3005 98.42 0.14608 0.14608 0.14528 0.1623 0.16078 0.1633 RANDOM 13.795
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] 1.78 -0.72 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.748 r_sphericity_free 3.273 r_scangle_it 3.25 r_scbond_it 2.181 r_sphericity_bonded 1.706 r_mcangle_it 1.486 r_angle_refined_deg 1.328 r_rigid_bond_restr 1.163 r_mcbond_it 0.901 r_angle_other_deg 0.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.748 r_sphericity_free 3.273 r_scangle_it 3.25 r_scbond_it 2.181 r_sphericity_bonded 1.706 r_mcangle_it 1.486 r_angle_refined_deg 1.328 r_rigid_bond_restr 1.163 r_mcbond_it 0.901 r_angle_other_deg 0.832 r_symmetry_vdw_other 0.332 r_nbd_other 0.241 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.107 r_symmetry_hbond_refined 0.105 r_symmetry_vdw_refined 0.093 r_chiral_restr 0.088 r_nbtor_other 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2340 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction CCP4 data scaling AMoRE phasing