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The crystal structure of cytochrome c' from Rubrivivax gelatinosus at 1.3 A Resolution and pH 8.0
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 VAPOR DIFFUSION, HANGING DROP 8 HANGING DROP 2.5 M AMMONIUM SULPHATE 0.1M TRIS-HCL PH8.0
Crystal Properties Matthews coefficient Solvent content 3.1 60.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.63 α = 90 b = 69.63 β = 90 c = 123.63 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 1996-10-10 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 1.29 19.94 99.8 0.04 33.7 5.1 87744
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 1.29 1.31 99.3 0.38 3.58 3.48
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 1.29 19.96 85947 1755 100 0.151 0.151 0.1609 0.179 0.1865 RANDOM 13.22
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] 0.64 0.32 0.64 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.434 r_dihedral_angle_4_deg 16.65 r_dihedral_angle_3_deg 11.422 r_dihedral_angle_1_deg 4.577 r_scangle_it 4.527 r_scbond_it 3.47 r_mcangle_it 2.395 r_mcbond_it 1.967 r_angle_refined_deg 1.744 r_angle_other_deg 1.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.434 r_dihedral_angle_4_deg 16.65 r_dihedral_angle_3_deg 11.422 r_dihedral_angle_1_deg 4.577 r_scangle_it 4.527 r_scbond_it 3.47 r_mcangle_it 2.395 r_mcbond_it 1.967 r_angle_refined_deg 1.744 r_angle_other_deg 1.019 r_nbd_refined 0.293 r_symmetry_vdw_other 0.199 r_symmetry_hbond_refined 0.195 r_nbtor_refined 0.192 r_xyhbond_nbd_refined 0.181 r_nbd_other 0.177 r_symmetry_vdw_refined 0.157 r_chiral_restr 0.096 r_nbtor_other 0.092 r_bond_refined_d 0.016 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 1804 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing