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Crystal Structure of a Beta-Lactamase-Like Protein from Brucella Melitensis bound to GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MD7 pdb entry 3md7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 290 15-18% PEG 3350, 200mM K/Na tartrate, 100mM BisTrisPropane pH 8.0, BrabA.11339.a.PW27637 at 18mg/ml supplemented with 1mM GMPPNP and 2mM MgCl2 at 18mg/ml, cryo: 21% PEG 3350, 15% EG, 165mM K/Na tartrate, 87mM BisTrisPropane pH 8.0, 1mM GMPPNP, 2mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.2 44.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.86 α = 90 b = 75.23 β = 90 c = 98.54 γ = 90
Symmetry Space Group C 2 2 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 RIGAKU SATURN 944+ 2010-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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 1.7 50 99.5 0.037 39.96 9.1 30143 29984 -3 17.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 93.1 0.147 0.147 9.1 4.4 2221
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 3md7 1.7 36.43 30143 29910 1542 99.2 0.141 0.141 0.14 0.148 0.168 0.1778 RANDOM 8.13
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] -0.15 -0.17 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.86 r_dihedral_angle_4_deg 15.196 r_dihedral_angle_3_deg 11.454 r_dihedral_angle_1_deg 6.165 r_scangle_it 3.172 r_scbond_it 1.98 r_angle_refined_deg 1.517 r_mcangle_it 1.215 r_angle_other_deg 0.936 r_mcbond_it 0.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.86 r_dihedral_angle_4_deg 15.196 r_dihedral_angle_3_deg 11.454 r_dihedral_angle_1_deg 6.165 r_scangle_it 3.172 r_scbond_it 1.98 r_angle_refined_deg 1.517 r_mcangle_it 1.215 r_angle_other_deg 0.936 r_mcbond_it 0.698 r_mcbond_other 0.209 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 2116 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 37
Software Software Software Name Purpose Structure data collection REFMAC refinement XDS data reduction XSCALE data scaling