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Crystal structure of an HIT-like protein from mycobacterium paratuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LB5 PDB entry 3LB5 modified with the CCP4 program CHAINSAW and truncated
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 EBS JCSG+ SCREEN G11: 100MM BISTRIS PH 6.5, 2M AMMONIUM SULPHATE; MYPAA.00754.B.A1 PS00728 AT 48MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.61 α = 90 b = 55.61 β = 90 c = 205.28 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 RIGAKU SATURN 944 2010-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 1.9 20 99 0.054 27.46 8.6 26492 26228 -3 26.91
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 1.9 1.95 91.2 0.362 2.7 2.9 1893
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 3LB5 modified with the CCP4 program CHAINSAW and truncated 1.9 20 26492 26020 1328 98.7 0.165 0.165 0.163 0.1683 0.206 0.2027 RANDOM 16.31
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] 0.69 0.69 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.829 r_dihedral_angle_4_deg 14.136 r_dihedral_angle_3_deg 11.759 r_dihedral_angle_1_deg 6.112 r_scangle_it 3.659 r_scbond_it 2.256 r_angle_refined_deg 1.462 r_mcangle_it 1.359 r_angle_other_deg 0.932 r_mcbond_it 0.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.829 r_dihedral_angle_4_deg 14.136 r_dihedral_angle_3_deg 11.759 r_dihedral_angle_1_deg 6.112 r_scangle_it 3.659 r_scbond_it 2.256 r_angle_refined_deg 1.462 r_mcangle_it 1.359 r_angle_other_deg 0.932 r_mcbond_it 0.747 r_mcbond_other 0.223 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2089 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 52
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling