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Triglycine variant of the Grp1 Pleckstrin Homology Domain unliganded
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 PEG 4000, sodium acetate, 10% glycerol, lithium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.794 α = 90 b = 107.514 β = 90 c = 37.359 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 2000-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 98.6 15937 15719 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.85 96.8
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 (All) 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 THROUGHOUT 1FGY 1.8 20 15086 14899 784 98.76 0.21897 0.21897 0.21786 0.226 0.24004 0.2483 RANDOM 23.028
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] -0.6 0.82 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.985 r_scangle_it 2.66 r_scbond_it 1.618 r_mcangle_it 1.424 r_angle_refined_deg 1.136 r_mcbond_it 0.766 r_angle_other_deg 0.724 r_symmetry_vdw_other 0.267 r_nbd_other 0.243 r_nbd_refined 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.985 r_scangle_it 2.66 r_scbond_it 1.618 r_mcangle_it 1.424 r_angle_refined_deg 1.136 r_mcbond_it 0.766 r_angle_other_deg 0.724 r_symmetry_vdw_other 0.267 r_nbd_other 0.243 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_refined 0.158 r_symmetry_hbond_refined 0.096 r_nbtor_other 0.082 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1057 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing