☰ Navigation Tabs
Structure of the yeast Pichia membranifaciens cytochrome c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YCC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.25 277 25% PEG 4000, 0.1 M Tris-HCl, pH 8.25
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.968 α = 90 b = 63.715 β = 90 c = 64.322 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 173 AREA DETECTOR SDMS 1990-12-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.4 15 95.8 0.177 0.161 0.223 0.133 0.951 3.2 2.2 4586
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 90.4 0.347 0.347 0.446 0.273 0.747 1.7 2.1
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 FREE R-VALUE 1ycc 2.4 15 4344 235 94.41 0.22197 0.21641 0.2248 0.33046 0.3368 RANDOM 38.586
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] -0.68 0.27 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.715 r_dihedral_angle_3_deg 14.985 r_dihedral_angle_1_deg 5.704 r_dihedral_angle_4_deg 5.468 r_long_range_B_refined 5.025 r_long_range_B_other 4.968 r_scangle_other 2.855 r_mcangle_it 2.259 r_mcangle_other 2.257 r_scbond_it 1.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.715 r_dihedral_angle_3_deg 14.985 r_dihedral_angle_1_deg 5.704 r_dihedral_angle_4_deg 5.468 r_long_range_B_refined 5.025 r_long_range_B_other 4.968 r_scangle_other 2.855 r_mcangle_it 2.259 r_mcangle_other 2.257 r_scbond_it 1.745 r_scbond_other 1.745 r_angle_refined_deg 1.674 r_mcbond_it 1.349 r_mcbond_other 1.34 r_angle_other_deg 0.628 r_chiral_restr 0.216 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 852 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DENZO data reduction Aimless data scaling PHASER phasing