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Crystal structure of the proaerolysin mutant Y221G complexed with mannose-6-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C0N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 291 9-11% PEG 4000, 100mM sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.954 α = 90 b = 90.78 β = 90 c = 165.805 γ = 90
Symmetry Space Group P 21 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 PIXEL PSI PILATUS 6M 2007-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.979 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 61.2 99.3 0.094 0.076 14.01 4.8 37597 37597
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 2.5 2.64 98.7 0.389 0.31 4.1 4.5 5385
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 3C0N 2.5 61.2 37534 1870 99.14 0.20658 0.20314 0.1974 0.27377 0.2588 RANDOM 23.63
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] -0.13 0.28 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.379 r_dihedral_angle_4_deg 21.909 r_dihedral_angle_3_deg 18.178 r_dihedral_angle_1_deg 7.241 r_mcangle_it 2.488 r_scangle_it 2.48 r_angle_refined_deg 2.005 r_scbond_it 1.664 r_mcbond_it 1.581 r_nbtor_refined 0.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.379 r_dihedral_angle_4_deg 21.909 r_dihedral_angle_3_deg 18.178 r_dihedral_angle_1_deg 7.241 r_mcangle_it 2.488 r_scangle_it 2.48 r_angle_refined_deg 2.005 r_scbond_it 1.664 r_mcbond_it 1.581 r_nbtor_refined 0.342 r_nbd_refined 0.259 r_symmetry_vdw_refined 0.24 r_xyhbond_nbd_refined 0.221 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.121 r_bond_refined_d 0.022 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7038 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing