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Crystal structure of a beta-lactamase-like protein bound to AMP from brucella melitensis, long wavelength synchrotron data
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 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 2.23 44.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.21 α = 90 b = 75.53 β = 90 c = 98.94 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 ADSC QUANTUM 315r 2010-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.3476 ALS 5.0.2
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 1.6 20 99.6 0.069 25.08 12.3 36517 36362 -3 20.91
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 1.6 1.64 95.9 0.39 5.8 6.1 36362
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 MR THROUGHOUT PDB entry 3md7 1.6 18.88 36362 36263 1868 99.4 0.145 0.145 0.143 0.1536 0.166 0.1794 RANDOM 10.64
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 -0.2 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.757 r_dihedral_angle_4_deg 16.3 r_dihedral_angle_3_deg 10.998 r_dihedral_angle_1_deg 6.181 r_scangle_it 4.038 r_scbond_it 2.549 r_mcangle_it 1.657 r_angle_refined_deg 1.652 r_angle_other_deg 0.983 r_mcbond_it 0.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.757 r_dihedral_angle_4_deg 16.3 r_dihedral_angle_3_deg 10.998 r_dihedral_angle_1_deg 6.181 r_scangle_it 4.038 r_scbond_it 2.549 r_mcangle_it 1.657 r_angle_refined_deg 1.652 r_angle_other_deg 0.983 r_mcbond_it 0.937 r_mcbond_other 0.286 r_chiral_restr 0.104 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 2118 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 40
Software Software Software Name Purpose BOS data collection REFMAC refinement XDS data reduction XSCALE data scaling