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Crystal structure of the single-stranded DNA binding protein from Mycobacterium leprae (Form II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AFP PDB ENTRY 3AFP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 298 0.1M HEPES, 3M NaCl, pH 7.5, microbatch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.486 α = 90 b = 102.486 β = 90 c = 120.762 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2006-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 30 99.7 0.059 15.3 2.4 18449 75.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 0.517 2 1810
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 PDB ENTRY 3AFP 2.8 30 17563 916 99.72 0.21246 0.21129 0.246 0.23545 0.2691 RANDOM 71.644
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] 3.41 3.41 -6.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.945 r_dihedral_angle_3_deg 18.189 r_dihedral_angle_4_deg 16.866 r_scangle_it 7.303 r_dihedral_angle_1_deg 5.888 r_mcangle_it 4.464 r_scbond_it 4.106 r_mcbond_it 2.663 r_angle_refined_deg 1.462 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.945 r_dihedral_angle_3_deg 18.189 r_dihedral_angle_4_deg 16.866 r_scangle_it 7.303 r_dihedral_angle_1_deg 5.888 r_mcangle_it 4.464 r_scbond_it 4.106 r_mcbond_it 2.663 r_angle_refined_deg 1.462 r_chiral_restr 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3165 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASES phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling