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Cytochrome C Peroxidase in complex with cyclopentane-carboximidamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 291 MES, MPD, pH 6.0, vapor diffusion, hanging drop, temperature 291K, pH 6.00
Crystal Properties Matthews coefficient Solvent content 3.09 60.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.898 α = 90 b = 74.925 β = 90 c = 106.968 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 110 CCD ADSC QUANTUM 315 KOHZU: DOUBLE CRYSTAL SI(111) 2007-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.8 50 99.4 0.053 33.2 4.3 38753
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 1.8 1.86 99.7 0.109 4
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1AC4 1.8 30 38433 38433 1929 99.4 0.161 0.159 0.195 0.223 RANDOM 15.24
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] 0.35 0.76 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.984 r_dihedral_angle_4_deg 23.695 r_dihedral_angle_3_deg 12.691 r_dihedral_angle_1_deg 6.41 r_scangle_it 2.934 r_scbond_it 2.048 r_angle_refined_deg 1.39 r_mcangle_it 1.271 r_mcbond_it 0.815 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.984 r_dihedral_angle_4_deg 23.695 r_dihedral_angle_3_deg 12.691 r_dihedral_angle_1_deg 6.41 r_scangle_it 2.934 r_scbond_it 2.048 r_angle_refined_deg 1.39 r_mcangle_it 1.271 r_mcbond_it 0.815 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.101 r_metal_ion_refined 0.074 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2340 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 51
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing