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Crystal structure of a Had-superfamily hydrolase from Ehrlichia chaffeensis at 1.9A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D6J pdb entry 3d6j modified with CCP4 program CHAINSAW and trimmed to conserved domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 HR INDEX SCREEN C6: 100MM BISTRIS PH 6.5, 1.5M AMMONIUM SULPHATE, 100MM NACL; EHCHA.01190.A AT 27MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.9 α = 90 b = 63.81 β = 90 c = 120.29 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 ADSC QUANTUM 315r 2009-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 50 99.2 0.077 14.54 3.9 21383 21206 -3 26.24
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 99.6 0.529 2.8 3.9 1531
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 3d6j modified with CCP4 program CHAINSAW and trimmed to conserved domain 1.9 33.95 21383 21161 1087 99.2 0.174 0.174 0.172 0.1832 0.213 0.2153 RANDOM 9.51
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] 0.22 0.75 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.908 r_dihedral_angle_4_deg 15.847 r_dihedral_angle_3_deg 13.907 r_dihedral_angle_1_deg 6.084 r_scangle_it 3.795 r_scbond_it 2.427 r_mcangle_it 1.523 r_angle_refined_deg 1.425 r_angle_other_deg 0.907 r_mcbond_it 0.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.908 r_dihedral_angle_4_deg 15.847 r_dihedral_angle_3_deg 13.907 r_dihedral_angle_1_deg 6.084 r_scangle_it 3.795 r_scbond_it 2.427 r_mcangle_it 1.523 r_angle_refined_deg 1.425 r_angle_other_deg 0.907 r_mcbond_it 0.842 r_mcbond_other 0.241 r_chiral_restr 0.093 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 1594 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 5
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling