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The crystal structure of almond HNL, PaHNL5 V317A, in complex with benzyl alcohol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Crystals of different forms were obtained under crystallization conditions varying - PEG 4K, isopropanol and 10mM Hepes pH 7-7.8 with protein concentration 19-28 mg/ml.
Crystal Properties Matthews coefficient Solvent content 2.59 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.364 α = 90 b = 95.161 β = 90.01 c = 92.19 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 PIXEL DECTRIS PILATUS 2M 2012-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 2.8 47.6 98.6 0.147 7.9 3.1 28768
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 2.8 2.97 97.8 0.564 2.5 3
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 (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 5EB4 2.8 47.58 27328 1439 98.65 0.22393 0.22209 0.2267 0.25884 0.2621 RANDOM 34.563
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] -2.46 0.28 7.84 -5.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.563 r_dihedral_angle_4_deg 14.868 r_dihedral_angle_3_deg 14.843 r_dihedral_angle_1_deg 5.502 r_long_range_B_refined 2.504 r_angle_refined_deg 1.214 r_mcangle_it 0.854 r_mcbond_it 0.469 r_scbond_it 0.38 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.563 r_dihedral_angle_4_deg 14.868 r_dihedral_angle_3_deg 14.843 r_dihedral_angle_1_deg 5.502 r_long_range_B_refined 2.504 r_angle_refined_deg 1.214 r_mcangle_it 0.854 r_mcbond_it 0.469 r_scbond_it 0.38 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7812 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 290
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing