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Crystal structure of the proaerolysin mutant Y221G at 2.2 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C0M
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 2.54 51.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.36 α = 90 b = 89.768 β = 90 c = 166.616 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 CCD MARRESEARCH 2006-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.95360 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 2.2 64.82 100 0.118 0.113 27.04 21.3 54407 54407
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 2.2 2.32 100 0.527 0.498 7.98 18.2 142371
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 3C0M 2.2 64.82 54335 2755 99.98 0.19164 0.18918 0.1963 0.23828 0.2371 RANDOM 19.383
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] -0.21 0.16 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.778 r_dihedral_angle_4_deg 18.236 r_dihedral_angle_3_deg 16.094 r_dihedral_angle_1_deg 6.859 r_scangle_it 4.39 r_scbond_it 2.873 r_mcangle_it 1.78 r_angle_refined_deg 1.727 r_mcbond_it 1.098 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.778 r_dihedral_angle_4_deg 18.236 r_dihedral_angle_3_deg 16.094 r_dihedral_angle_1_deg 6.859 r_scangle_it 4.39 r_scbond_it 2.873 r_mcangle_it 1.78 r_angle_refined_deg 1.727 r_mcbond_it 1.098 r_nbtor_refined 0.313 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.162 r_chiral_restr 0.118 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7039 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing