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Co-crystal structure of human UNC119 (retina gene 4) and an N-terminal Transducin-alpha mimicking peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GQQ PDB ENTRY 3GQQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 5 277 40% PEG 5000, 0.1 M sodium acetate, 0.1 M potassium acetate, 30% isopropanol, pH 5.0, LIQUID DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.06 40.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.546 α = 90 b = 79.713 β = 90 c = 189.59 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 MARMOSAIC 325 mm CCD 2010-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9749 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.988 30 100 0.116 11 15.2 82342
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.988 2.07 100 0.701 0.701 2.1 10.3
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 (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 ENTRY 3GQQ 2 29.37 78089 77030 4087 99.96 0.19134 0.18845 0.1891 0.24557 0.2448 RANDOM 30.833
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] 0.24 0.7 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.778 r_dihedral_angle_4_deg 17.78 r_dihedral_angle_3_deg 14.773 r_dihedral_angle_1_deg 6.252 r_scangle_it 5.441 r_scbond_it 3.452 r_mcangle_it 2.322 r_angle_refined_deg 1.843 r_mcbond_it 1.339 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.778 r_dihedral_angle_4_deg 17.78 r_dihedral_angle_3_deg 14.773 r_dihedral_angle_1_deg 6.252 r_scangle_it 5.441 r_scbond_it 3.452 r_mcangle_it 2.322 r_angle_refined_deg 1.843 r_mcbond_it 1.339 r_chiral_restr 0.15 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 8494 Nucleic Acid Atoms Solvent Atoms 793 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing