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Crystal structure of putative peptidase M23 from pseudomonas aeruginosa, New York Structural Genomics Consortium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GU1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 100 MM HEPES, 0.2 M AMMONIUM ACETATE, 25% PEG 3350, 10% GLYCEROL, PH 6.50, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.3 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.313 α = 90 b = 108.313 β = 90 c = 83.181 γ = 120
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 IV MIRRORS 2006-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.9 50 99.9 0.065 0.048 9.4 6.1 43712
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) 1.9 1.97 100 0.46 0.46 2.2 5.4
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 2GU1 1.9 20 42302 1360 99.98 0.20545 0.20419 0.2033 0.24522 0.2413 RANDOM 29.676
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] 0.36 0.18 0.36 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.598 r_dihedral_angle_3_deg 14.602 r_dihedral_angle_4_deg 12.153 r_scangle_it 7.839 r_dihedral_angle_1_deg 7.165 r_scbond_it 5.566 r_mcangle_it 4.375 r_mcbond_it 3.687 r_angle_refined_deg 1.327 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.598 r_dihedral_angle_3_deg 14.602 r_dihedral_angle_4_deg 12.153 r_scangle_it 7.839 r_dihedral_angle_1_deg 7.165 r_scbond_it 5.566 r_mcangle_it 4.375 r_mcbond_it 3.687 r_angle_refined_deg 1.327 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.164 r_nbd_refined 0.145 r_symmetry_vdw_refined 0.132 r_chiral_restr 0.107 r_metal_ion_refined 0.035 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_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 3484 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 2
Software Software Software Name Purpose PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling