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High resolution crystal structure of histidine triad nucleotide-binding protein 1 (Hint1) C84A mutant from rabbit complexed with adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LLJ PDB ENTRY 3LLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 281 30% PEG 8000, 0.1M sodium cacodylate pH 6.5, O.1M sodium acetate, protein concentration 10 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.04 39.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.765 α = 90 b = 39.765 β = 90 c = 141.41 γ = 90
Symmetry Space Group P 43 21 2
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 MAR CCD 165 mm mirrors 2009-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.0379 MAX II I911-2
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 1.08 50 99.6 0.11 16.15 10.7 49845 -3 11
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) 1.08 1.1 99.7 0.628 2.88 7.3 2434
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3LLJ 1.08 23.05 49924 47232 2522 99.68 0.14296 0.14296 0.14146 0.1399 0.17139 0.1662 RANDOM 23.216
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] 0.11 0.11 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.686 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_4_deg 10.595 r_scangle_it 6.684 r_dihedral_angle_1_deg 6.219 r_scbond_it 4.802 r_mcangle_it 3.808 r_mcbond_it 2.664 r_rigid_bond_restr 2.583 r_angle_refined_deg 2.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.686 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_4_deg 10.595 r_scangle_it 6.684 r_dihedral_angle_1_deg 6.219 r_scbond_it 4.802 r_mcangle_it 3.808 r_mcbond_it 2.664 r_rigid_bond_restr 2.583 r_angle_refined_deg 2.272 r_chiral_restr 0.136 r_bond_refined_d 0.025 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 883 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 20
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling