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Structure of a peptide derived from Cdc9 bound to PCNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PLQ PDB entry 1PLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 294 1.6 M (NH4)2SO4, Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.58 65.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.28 α = 90 b = 139.28 β = 90 c = 139.28 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 Vertical focusing mirror 2002-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97900 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.8 40 99.2 0.039 0.039 5 4.4 11287 11287 94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 99.2 0.418 0.418 2 3.1 1104
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1PLQ 2.8 29.7 11219 10682 537 99.75 0.24865 0.24681 0.28527 0.3001 RANDOM 27.318
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.102 r_dihedral_angle_4_deg 19.664 r_dihedral_angle_3_deg 16.997 r_dihedral_angle_1_deg 6.097 r_angle_refined_deg 1.081 r_scangle_it 0.879 r_mcangle_it 0.607 r_scbond_it 0.525 r_mcbond_it 0.338 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.102 r_dihedral_angle_4_deg 19.664 r_dihedral_angle_3_deg 16.997 r_dihedral_angle_1_deg 6.097 r_angle_refined_deg 1.081 r_scangle_it 0.879 r_mcangle_it 0.607 r_scbond_it 0.525 r_mcbond_it 0.338 r_nbtor_refined 0.313 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.168 r_nbd_refined 0.16 r_symmetry_vdw_refined 0.125 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2095 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection MOSFLM data reduction CCP4 data scaling AMoRE phasing