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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 2.19 43.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.383 α = 90 b = 37.538 β = 90 c = 38.534 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 1998-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 97.8 0.1 6.4 5.3 8677 23.1
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 85.6
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 8648 428 97.8 0.198 0.198 0.26 RANDOM 25.3
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 27.1 x_scangle_it 4.72 x_mcangle_it 3.06 x_scbond_it 2.98 x_mcbond_it 1.86 x_angle_deg 1.6 x_improper_angle_d 0.75 x_bond_d 0.01 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 27.1 x_scangle_it 4.72 x_mcangle_it 3.06 x_scbond_it 2.98 x_mcbond_it 1.86 x_angle_deg 1.6 x_improper_angle_d 0.75 x_bond_d 0.01 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 971 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 18
Software Software Software Name Purpose X-PLOR refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing