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Crystal structure of Amidohydrolase from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 Internal tracking number 226312A8 (JCSG A8).
Crystallant: 20% PEG3350, 200 mM ammonium formate.
Protein: BrabA.17379.a.A1 PS01212 at 36.85 mg/ml in a buffer consisting
of 25 mM Hepes pH 7.0, 500 mM NaCl, 2 mM DTT, 0.025% sodium azide, and 5% glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.15 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.592 α = 92.75 b = 62.192 β = 95.49 c = 68.926 γ = 112.32
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 315 2011-12-18 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 2.05 50 97.9 0.086 8.4 2.2 49766
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 2.05 2.09 96.5 0.211 3.8 2.2 2456
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 3MDU 2.05 50 49766 2531 97.57 0.15 0.148 0.1553 0.184 0.187 RANDOM 21.396
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] -0.07 -0.18 0.08 -0.48 -0.28 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.318 r_dihedral_angle_4_deg 15.383 r_dihedral_angle_3_deg 12.328 r_dihedral_angle_1_deg 6.107 r_angle_refined_deg 1.418 r_angle_other_deg 1.119 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.318 r_dihedral_angle_4_deg 15.383 r_dihedral_angle_3_deg 12.328 r_dihedral_angle_1_deg 6.107 r_angle_refined_deg 1.418 r_angle_other_deg 1.119 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6762 Nucleic Acid Atoms Solvent Atoms 619 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction