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THE CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RUBRIVIVAX GELATINOSUS AT 1.5 A RESOLUTION AND PH 6.3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JAF PDB ENTRY 1JAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 2.4M AMMONIUM SULPHATE 0.1M SODIUM CITRATE PH6.3
Crystal Properties Matthews coefficient Solvent content 3.1 60.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.558 α = 90 b = 69.558 β = 90 c = 123.374 γ = 120
Symmetry Space Group P 31 2 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 1999-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.5 19.9 99.4 0.05 29.8 9.8 55765
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 1.5 1.53 99.2 0.22 8.2 15.4
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 1JAF 1.5 19.92 54533 1134 100 0.153 0.153 0.1651 0.177 0.1851 RANDOM 14.93
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] 0.5 0.25 0.5 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.794 r_dihedral_angle_4_deg 16.836 r_dihedral_angle_3_deg 11.148 r_dihedral_angle_1_deg 4.513 r_scangle_it 4.43 r_scbond_it 3.335 r_mcangle_it 2.23 r_mcbond_it 1.799 r_angle_refined_deg 1.582 r_angle_other_deg 1.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.794 r_dihedral_angle_4_deg 16.836 r_dihedral_angle_3_deg 11.148 r_dihedral_angle_1_deg 4.513 r_scangle_it 4.43 r_scbond_it 3.335 r_mcangle_it 2.23 r_mcbond_it 1.799 r_angle_refined_deg 1.582 r_angle_other_deg 1.087 r_symmetry_hbond_refined 0.399 r_nbd_refined 0.294 r_chiral_restr 0.204 r_nbtor_refined 0.189 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.137 r_symmetry_vdw_refined 0.131 r_symmetry_vdw_other 0.125 r_nbtor_other 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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 1792 Nucleic Acid Atoms Solvent Atoms 456 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing