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Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10-25% PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.76 55.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.881 α = 90 b = 171.71 β = 90 c = 89.363 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS V 2004-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.0000 SPring-8 BL32B2
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 2.85 30 99.8 0.061 17.1 5.7 39032 79.773
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) 2.85 2.95 0.998 0.232 5.7 5.5
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1QME 2.85 30 37041 1961 99.72 0.22686 0.22381 0.28568 RANDOM 66.58
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] 0.87 -2.98 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.984 r_dihedral_angle_3_deg 16.654 r_dihedral_angle_4_deg 14.686 r_dihedral_angle_1_deg 5.522 r_scangle_it 1.144 r_angle_refined_deg 1.067 r_mcangle_it 0.78 r_scbond_it 0.682 r_mcbond_it 0.431 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.984 r_dihedral_angle_3_deg 16.654 r_dihedral_angle_4_deg 14.686 r_dihedral_angle_1_deg 5.522 r_scangle_it 1.144 r_angle_refined_deg 1.067 r_mcangle_it 0.78 r_scbond_it 0.682 r_mcbond_it 0.431 r_nbtor_refined 0.299 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9797 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement BSS data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing