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Crystal structure of conserved protein of unknown function DIP1874 from Corynebacterium diphtheriae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAD phased model of the L37M mutant of the same protein, P1 space group
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.7 295 30% PEG 8000, 0.1 M Acetate pH 4.5, 0.2 M Lithium sulfate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.59 52.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.374 α = 90 b = 59.374 β = 90 c = 98.948 γ = 90
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 SBC-3 Mirrors 2007-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.98 50.9 97.3 0.049 12.3 11.7 11597 11597 41
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) 1 1.98 2.05 76.4 0.297 5.77 8.6 905
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD phased model of the L37M mutant of the same protein, P1 space group 2 29.68 11027 11027 549 99.46 0.19 0.19 0.188 0.1849 0.229 0.2208 RANDOM 38.883
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] 0.52 0.52 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.438 r_dihedral_angle_4_deg 26.74 r_dihedral_angle_3_deg 16.494 r_dihedral_angle_1_deg 7.819 r_scangle_it 3.761 r_scbond_it 2.546 r_mcangle_it 2.205 r_angle_refined_deg 1.76 r_mcbond_it 1.361 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.438 r_dihedral_angle_4_deg 26.74 r_dihedral_angle_3_deg 16.494 r_dihedral_angle_1_deg 7.819 r_scangle_it 3.761 r_scbond_it 2.546 r_mcangle_it 2.205 r_angle_refined_deg 1.76 r_mcbond_it 1.361 r_nbtor_refined 0.312 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.219 r_xyhbond_nbd_refined 0.213 r_symmetry_hbond_refined 0.163 r_chiral_restr 0.129 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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_refined 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 1028 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing