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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 5.2 20MM SODIUM CITRATE, 0.2M SODIUM POTASSIUM TARTARATE, 10% PEG 6000 PH 5.2
Crystal Properties Matthews coefficient Solvent content 1.89 35.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.021 α = 90 b = 37.778 β = 90 c = 32.973 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 100 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 30 91.1 0.085 9.6 5.3 6973 14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.06 78.4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1B1I 2 20 6947 384 91 0.235 0.235 0.287 RANDOM 26.9
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] -8.46 -2.29 10.75
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 2.54 c_mcangle_it 2.14 c_scbond_it 1.73 c_angle_deg 1.5 c_mcbond_it 1.28 c_improper_angle_d 1 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 2.54 c_mcangle_it 2.14 c_scbond_it 1.73 c_angle_deg 1.5 c_mcbond_it 1.28 c_improper_angle_d 1 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 984 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 9
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing