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Structure of human ADP-ribosylation factor-like 5 (ARL5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z6Y pdb entry 1z6y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 2.0M sodium formate, 0.1M BTP, pH 7.0, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.98 37.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.047 α = 90 b = 48.772 β = 90 c = 85.711 γ = 90
Symmetry Space Group P 21 21 21
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 210 2005-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.97895 APS 17-ID
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 1.7 28.72 98.9 0.055 11.7 6.9 18505
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) 1.7 1.76 97.6 0.475 5.6
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 1z6y 1.7 28.72 18430 938 98.889 0.188 0.1856 0.1933 0.2267 0.234 random 17.799
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] -0.62 -0.5 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.205 r_dihedral_angle_4_deg 16.392 r_dihedral_angle_3_deg 11.122 r_dihedral_angle_1_deg 5.883 r_scangle_it 4.822 r_mcangle_it 3.723 r_scbond_it 3.204 r_mcbond_it 3.106 r_angle_refined_deg 1.469 r_angle_other_deg 1.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.205 r_dihedral_angle_4_deg 16.392 r_dihedral_angle_3_deg 11.122 r_dihedral_angle_1_deg 5.883 r_scangle_it 4.822 r_mcangle_it 3.723 r_scbond_it 3.204 r_mcbond_it 3.106 r_angle_refined_deg 1.469 r_angle_other_deg 1.052 r_mcbond_other 0.728 r_symmetry_vdw_other 0.345 r_nbd_refined 0.213 r_nbd_other 0.206 r_nbtor_refined 0.171 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.114 r_chiral_restr 0.094 r_nbtor_other 0.077 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1314 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 31
Software Software Software Name Purpose PHASER phasing DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ARP/wARP model building MolProbity model building