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Crystal structure of human gamma-tubulin bound to GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z5V PDB 1Z5V stripped of sidechains and ligands
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.2 298 top solution: 83 mM HEPES pH 7.2, 1.2M KCl, 20% PEG6000, 1mM GDP;
reservoir: 83mM HEPES pH 7.2, 0.6M KCl, 20% PEG6000, 1 mM GDP.
Protein was mixed 1:1 or 1:2 with top solution, and equilibrated over the reservoir solution., VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 42.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.744 α = 90 b = 108.755 β = 96.33 c = 83.347 γ = 90
Symmetry Space Group P 1 21 1
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 315 2005-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
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 2.303 82.76 98.9 40179 38587 -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) 2.303 2.38 97
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 PDB 1Z5V stripped of sidechains and ligands 2.303 82.76 38587 38151 2005 98.87 0.18908 0.18908 0.18654 0.1863 0.23786 0.2391 RANDOM 25.015
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] -0.08 -0.07 0.71 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.055 r_dihedral_angle_4_deg 17.371 r_dihedral_angle_3_deg 15.388 r_dihedral_angle_1_deg 5.388 r_scangle_it 1.847 r_scbond_it 1.154 r_angle_refined_deg 1.149 r_mcangle_it 0.965 r_mcbond_it 0.565 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.055 r_dihedral_angle_4_deg 17.371 r_dihedral_angle_3_deg 15.388 r_dihedral_angle_1_deg 5.388 r_scangle_it 1.847 r_scbond_it 1.154 r_angle_refined_deg 1.149 r_mcangle_it 0.965 r_mcbond_it 0.565 r_nbtor_refined 0.299 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6578 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 56
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling