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Crystal structure of mutant D471N of the periplasmic domain of CadC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 20% (w/v) PEG 6000, 0.1 M Na citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.73 α = 90 b = 79.73 β = 90 c = 126.01 γ = 120
Symmetry Space Group P 32 2 1
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 RAYONIX MX-225 mirrors 2009-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 2.2 69.05 99.8 0.052 20.2 24083 -3 44.262
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) 2.2 2.3 99.9 0.367 4.6 5.1 2963
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 (All) 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 3LY7 2.2 69.05 24043 1228 99.61 0.23 0.23 0.228 0.1984 0.279 0.2482 RANDOM 33.603
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] -1.45 -0.73 -1.45 2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.399 r_dihedral_angle_4_deg 19.086 r_dihedral_angle_3_deg 14.131 r_dihedral_angle_1_deg 5.865 r_scangle_it 4.049 r_scbond_it 2.661 r_mcangle_it 1.757 r_angle_refined_deg 1.513 r_mcbond_it 0.966 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.399 r_dihedral_angle_4_deg 19.086 r_dihedral_angle_3_deg 14.131 r_dihedral_angle_1_deg 5.865 r_scangle_it 4.049 r_scbond_it 2.661 r_mcangle_it 1.757 r_angle_refined_deg 1.513 r_mcbond_it 0.966 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2556 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection