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Crystal structure of human TBC1 domain family member 22A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G77 PDB entry 2G77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 28.0% PEG400, 0.2M Calcium chloride, 0.1M Sodium HEPES, pH 7.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.5 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.911 α = 90 b = 121.515 β = 93.64 c = 66.278 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 4 2007-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 1.1000 NSLS X12B
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 2.1 30 100 0.152 6.5 6.4 39313
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) 2.1 2.18 100 0.966 6.1
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 2G77 2.1 30 39184 2049 99.187 0.205 0.2021 0.2101 0.2571 0.2596 thin shells 25.763
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] 0.597 -1.056 -0.924 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.673 r_dihedral_angle_4_deg 18.829 r_dihedral_angle_3_deg 14.573 r_dihedral_angle_1_deg 5.574 r_mcangle_it 3.883 r_scangle_it 3.786 r_scbond_it 2.776 r_mcbond_it 2.742 r_angle_refined_deg 1.395 r_angle_other_deg 0.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.673 r_dihedral_angle_4_deg 18.829 r_dihedral_angle_3_deg 14.573 r_dihedral_angle_1_deg 5.574 r_mcangle_it 3.883 r_scangle_it 3.786 r_scbond_it 2.776 r_mcbond_it 2.742 r_angle_refined_deg 1.395 r_angle_other_deg 0.993 r_mcbond_other 0.77 r_nbd_refined 0.206 r_nbd_other 0.185 r_nbtor_refined 0.181 r_symmetry_vdw_refined 0.155 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.149 r_symmetry_vdw_other 0.14 r_nbtor_other 0.087 r_chiral_restr 0.083 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4900 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection