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Crystal structure of putative amidohydrolase BH0493 from Bacillus halodurans C-125
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q08 PDB entry 2Q08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 0.1M Bis-Tris pH 6.5, 45% PPG P 400 (INDEX E10), VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.96 58.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.995 α = 78.85 b = 122.208 β = 78.95 c = 127.582 γ = 80.92
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 SGX-CAT 2007-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97900 APS 31-ID
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 1.65 50 88.5 0.044 12.6 2.1 759838
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) 1.65 1.71 49.1 0.384 1.5 42180
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 PDB entry 2Q08 1.65 19.99 759011 37962 89.62 0.189 0.187 0.1866 0.224 0.2231 RANDOM 26.888
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.476 r_dihedral_angle_4_deg 18.91 r_dihedral_angle_3_deg 13.342 r_scbond_it 6.861 r_dihedral_angle_1_deg 6.402 r_scangle_it 4.416 r_mcangle_it 3.734 r_angle_refined_deg 1.604 r_mcbond_it 1.456 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.476 r_dihedral_angle_4_deg 18.91 r_dihedral_angle_3_deg 13.342 r_scbond_it 6.861 r_dihedral_angle_1_deg 6.402 r_scangle_it 4.416 r_mcangle_it 3.734 r_angle_refined_deg 1.604 r_mcbond_it 1.456 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.214 r_metal_ion_refined 0.187 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41373 Nucleic Acid Atoms Solvent Atoms 4909 Heterogen Atoms 32
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHASER phasing