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Structure of Human ADP-ribosylation factor-like 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PEG 3350, Sodium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.725 α = 90 b = 48.137 β = 103.45 c = 51.371 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 IMAGE PLATE RIGAKU RAXIS IV 2005-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 30 99.9 0.077 3.4 12238 12238 21.4
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 2.07 100 0.211 3.5 2.16 1220
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RRF 2 30 12228 11611 617 99.9 0.2261 0.2261 0.226 0.2343 0.27 RANDOM 21.581
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] -0.57 0.55 -0.16 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.481 r_dihedral_angle_4_deg 23.474 r_dihedral_angle_3_deg 15.445 r_dihedral_angle_1_deg 6.096 r_scangle_it 2.79 r_scbond_it 1.973 r_angle_refined_deg 1.509 r_mcangle_it 1.405 r_mcbond_it 0.909 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.481 r_dihedral_angle_4_deg 23.474 r_dihedral_angle_3_deg 15.445 r_dihedral_angle_1_deg 6.096 r_scangle_it 2.79 r_scbond_it 1.973 r_angle_refined_deg 1.509 r_mcangle_it 1.405 r_mcbond_it 0.909 r_nbtor_refined 0.304 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.215 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.109 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1341 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 28
Software Software Software Name Purpose CrystalClear data collection CrystalClear data reduction AMoRE phasing REFMAC refinement CrystalClear data scaling