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Crystal structure of a beta-lactamase-like protein from brucella melitensis bound to AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MD7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 290 5-18% PEG 3350, 200mM K/Na tartrate, 100mM BisTrisPropane pH 8.0, BrabA.11339.a.PW27637 at 18mg/ml supplemented with 1mM AMPPNP and 2mM MgCl2 at 18mg/ml. Cryo: 21% PEG 3350, 15% EG, 165mM K/Na tartrate, 87mM BisTrisPropane pH 8.0, 1mM AMPPNP, 2mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.2 43.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.85 α = 90 b = 75.2 β = 90 c = 98.53 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+ 2010-12-03 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 0.041 35.24 9.1 30108 29964 -3 20.88
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 1.7 1.74 93.6 0.203 7.7 4.5 2210
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 3md7 1.7 46.21 30108 29890 1539 99.3 0.164 0.164 0.163 0.1685 0.196 0.2022 RANDOM 10.44
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] -0.2 -0.27 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.253 r_dihedral_angle_4_deg 16.169 r_dihedral_angle_3_deg 11.238 r_dihedral_angle_1_deg 6.297 r_scangle_it 3.219 r_scbond_it 2.133 r_angle_refined_deg 1.639 r_mcangle_it 1.287 r_angle_other_deg 0.976 r_mcbond_it 0.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.253 r_dihedral_angle_4_deg 16.169 r_dihedral_angle_3_deg 11.238 r_dihedral_angle_1_deg 6.297 r_scangle_it 3.219 r_scbond_it 2.133 r_angle_refined_deg 1.639 r_mcangle_it 1.287 r_angle_other_deg 0.976 r_mcbond_it 0.808 r_mcbond_other 0.284 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 2110 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 36
Software Software Software Name Purpose Structure data collection REFMAC refinement XDS data reduction XSCALE data scaling