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Binding of Phosphate and Pyrophosphate ions at the active site of human angiogenin as revealed by X-ray Crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B1I PDB ENTRY 1B1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 25% PEG 6000, 0.1M MES, PH 6.0, 0.1M NACL
Crystal Properties Matthews coefficient Solvent content 1.97 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.206 α = 90 b = 38.405 β = 90 c = 33.568 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 IMAGE PLATE MARRESEARCH MIRRORS 1998-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.5 SRS PX9.5
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 2 40 92.9 0.079 20 5.3 7458 19.6
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 2 2.06 97.1 0.152 11.2 2.5
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1B1I 2 40 7447 566 93.1 0.185 0.185 0.23 RANDOM 24.7
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 x_dihedral_angle_d 27.8 x_scangle_it 7.02 x_mcangle_it 4.67 x_scbond_it 4.66 x_mcbond_it 3 x_angle_deg 1.4 x_improper_angle_d 0.77 x_bond_d 0.009 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 27.8 x_scangle_it 7.02 x_mcangle_it 4.67 x_scbond_it 4.66 x_mcbond_it 3 x_angle_deg 1.4 x_improper_angle_d 0.77 x_bond_d 0.009 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 992 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 5
Software Software Software Name Purpose X-PLOR refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing