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Crystal structure of a Phosphate Binding Protein (PBP-1) from Clostridium perfringens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GD5 PDB ENTRY 4GD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 60 mg/mL protein, 0.1 N sodium acetate, pH 4.5, 0.2 M zinc acetate, 10% PEG3000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.78 α = 90 b = 105.73 β = 90 c = 146.45 γ = 90
Symmetry Space Group F 2 2 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 PIXEL DECTRIS PILATUS 6M 2012-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.8000 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 37.564 99.9 33131 33131 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 100
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 PDB ENTRY 4GD5 1.65 37.564 31475 1657 99.9 0.13474 0.13239 0.1416 0.17843 0.1804 RANDOM 33.254
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] 0.6 -1.3 0.7
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.001 r_dihedral_angle_2_deg 35.826 r_sphericity_bonded 20.836 r_dihedral_angle_3_deg 13.665 r_dihedral_angle_4_deg 12.46 r_rigid_bond_restr 8.864 r_long_range_B_refined 6.227 r_scangle_other 5.951 r_dihedral_angle_1_deg 5.861 r_long_range_B_other 5.549
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.001 r_dihedral_angle_2_deg 35.826 r_sphericity_bonded 20.836 r_dihedral_angle_3_deg 13.665 r_dihedral_angle_4_deg 12.46 r_rigid_bond_restr 8.864 r_long_range_B_refined 6.227 r_scangle_other 5.951 r_dihedral_angle_1_deg 5.861 r_long_range_B_other 5.549 r_scbond_other 5.322 r_scbond_it 5.313 r_mcangle_other 3.782 r_mcangle_it 3.778 r_mcbond_other 3.287 r_mcbond_it 3.27 r_angle_other_deg 2.903 r_angle_refined_deg 1.944 r_chiral_restr 0.135 r_bond_refined_d 0.02 r_gen_planes_other 0.013 r_gen_planes_refined 0.008 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1818 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 9
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling