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Crystal structure of P99 beta-lactamase in complex with a penicillin derivative MPC-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1M Bis-Tris pH 6.5, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.16 α = 90 b = 69.33 β = 90 c = 76.85 γ = 90
Symmetry Space Group P 2 21 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 2016-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.91836 SSRF BL17B1
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 1.74 69.33 99.4 0.087 13.3 6.8 30924
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 1.8 1.9 99.4 0.292 0.292 6.2 6.8
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 1XX2 1.8 69 29328 1559 99.73 0.21289 0.21181 0.2191 0.2331 0.2408 RANDOM 11.994
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] 0.02 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.468 r_dihedral_angle_3_deg 16.25 r_dihedral_angle_4_deg 16.164 r_dihedral_angle_1_deg 7.108 r_long_range_B_refined 4.689 r_long_range_B_other 4.683 r_scangle_other 3.777 r_scbond_it 2.437 r_scbond_other 2.437 r_mcangle_it 1.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.468 r_dihedral_angle_3_deg 16.25 r_dihedral_angle_4_deg 16.164 r_dihedral_angle_1_deg 7.108 r_long_range_B_refined 4.689 r_long_range_B_other 4.683 r_scangle_other 3.777 r_scbond_it 2.437 r_scbond_other 2.437 r_mcangle_it 1.753 r_mcangle_other 1.753 r_angle_refined_deg 1.211 r_mcbond_it 1.152 r_mcbond_other 1.149 r_angle_other_deg 0.676 r_chiral_restr 0.075 r_gen_planes_refined 0.012 r_bond_refined_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2751 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing