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X-ray structure of the M100K variant of ferric cyt c-550 from Paracoccus versutus determined at 295 K.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1COT PDB ENTRY 1COT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 3.2 M AMMONIUM SULFATE, 0.1 M BICINE PH 9
Crystal Properties Matthews coefficient Solvent content 2 38.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.457 α = 90 b = 43.011 β = 90 c = 87.954 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 295 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2003-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR78
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 1.95 43.85 99.3 0.12 13.6 6.2 9207 2
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 1.95 1.99 92.5 0.39 2.8 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1COT 1.95 43.85 8711 434 99.3 0.187 0.185 0.1911 0.233 0.2322 RANDOM 33.58
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] 1.26 1.52 -2.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.57 r_dihedral_angle_4_deg 16.249 r_dihedral_angle_3_deg 16.012 r_dihedral_angle_1_deg 5.07 r_scangle_it 2.558 r_mcangle_it 2.491 r_mcbond_it 2.14 r_scbond_it 1.835 r_angle_refined_deg 1.153 r_angle_other_deg 0.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.57 r_dihedral_angle_4_deg 16.249 r_dihedral_angle_3_deg 16.012 r_dihedral_angle_1_deg 5.07 r_scangle_it 2.558 r_mcangle_it 2.491 r_mcbond_it 2.14 r_scbond_it 1.835 r_angle_refined_deg 1.153 r_angle_other_deg 0.663 r_nbd_refined 0.277 r_symmetry_hbond_refined 0.205 r_nbtor_refined 0.185 r_nbd_other 0.183 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.136 r_nbtor_other 0.091 r_symmetry_vdw_other 0.083 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 914 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing