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Structure of human ADP-ribosylation factor 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z6X PDB entry 1Z6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 25% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate, 3% 6-aminocaproic acid, pH 4.6, vapor diffusion, sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.9 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.996 α = 90 b = 81.64 β = 90 c = 84.399 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV 2005-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 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 1.76 50 98.8 0.068 5.9 22373
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 1.76 1.9 95.6 0.306 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT PDB entry 1Z6X 1.764 32.5 22352 1147 99.347 0.202 0.2005 0.2103 0.236 0.2409 RANDOM 15.61
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] -0.394 0.6 -0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.78 r_dihedral_angle_4_deg 13.126 r_dihedral_angle_3_deg 11.204 r_dihedral_angle_1_deg 5.87 r_scangle_it 3.527 r_mcangle_it 2.998 r_scbond_it 2.595 r_mcbond_it 2.301 r_mcangle_other 1.799 r_scangle_other 1.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.78 r_dihedral_angle_4_deg 13.126 r_dihedral_angle_3_deg 11.204 r_dihedral_angle_1_deg 5.87 r_scangle_it 3.527 r_mcangle_it 2.998 r_scbond_it 2.595 r_mcbond_it 2.301 r_mcangle_other 1.799 r_scangle_other 1.765 r_angle_refined_deg 1.4 r_scbond_other 0.894 r_angle_other_deg 0.778 r_mcbond_other 0.723 r_symmetry_vdw_other 0.274 r_symmetry_vdw_refined 0.265 r_nbd_refined 0.213 r_nbd_other 0.191 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.081 r_nbtor_other 0.08 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1345 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction